Flow Cytometry Protocols [2 ed.] 1588292355, 9781588292353

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Flow Cytometry Protocols

M E T H O D S I N M O L E C U L A R B I O L O G Y™

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M E T H O D S I N M O L E C U L A R B I O L O G Y™

Flow Cytometry Protocols SECOND EDITION Edited by

Teresa S. Hawley American Red Cross, Rockville, MD

Robert G. Hawley American Red Cross, Rockville, MD The George Washington University, Washington, DC

© 2004 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.humanapress.com All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Methods in Molecular BiologyTM is a trademark of The Humana Press Inc. All papers, comments, opinions, conclusions, or recommendatoins are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. ∞ ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Cover design by Patricia F. Cleary. Cover illustrations: (Background) Red fluorescent protein-expressing fibroblasts (T.S. Hawley and R.G. Hawley). (Foreground ) Analysis of a mixture of ten hybridoma cell lines expressing different combinations of four fluorescent protein variants. Representative bivariate histograms illustrating the hyper-log transform (top row) and FCOM histogram showing all signal combinations (bottom row), generated with WinList v5.0 prerelease software (Verity Software House, Topsham, ME). Data from T. S. Hawley et al. (Chapter 12). Figure prepared by C. Bruce Bagwell (Verity Software House). For additional copies, pricing for bulk purchases, and/or information about other Humana titles, contact Humana at the above address or at any of the following numbers: Tel.: 973-256-1699; Fax: 973-256-8341; E-mail: [email protected]; or visit our Website: www.humanapress.com Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Humana Press Inc., provided that the base fee of US $25.00 per copy is paid directly to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [1-58829-234-7/04 $25.00 ]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 ISSN: 1064-3745 E-ISBN: 1-059259-773-4 Library of Congress Cataloging-in-Publication Data Flow cytometry protocols.-- 2nd ed. / edited by Teresa S. Hawley, Robert G. Hawley. p. ; cm. -- (Methods in molecular biology, ISSN 1064-3745 ; 263) Includes bibliographical references and index. ISBN 1-58829-234-7 (hardcover : alk. paper) -- ISBN 1-58829-235-5 (pbk. : alk. paper) 1. Flow cytometry--Laboratory manuals. [DNLM: 1. Flow Cytometry--methods. QH 585.5.F56 F6447 2004] I. Hawley, Teresa S. II. Hawley, Robert G. III. Series: Methods in molecular biology (Clifton, N.J.) ; v. 263. QH585.5.F56F587 2004 611'.0181'0284--dc22 2003027882

Preface Flow cytometry has evolved since the 1940s into a multidisciplinary field incorporating aspects of laser technology, fluid dynamics, electronics, optics, computer science, physics, chemistry, biology, and mathematics. Innovations in instrumentation, development of small lasers, discovery of new fluorochromes/fluorescent proteins, and implementation of novel methodologies have all contributed to the recent rapid expansion of flow cytometry applications. In this thoroughly revised and updated second edition of Flow Cytometry Protocols, time-proven as well as cutting-edge methods are clearly and comprehensively presented by leading experimentalists. In addition to being a valuable reference manual for experienced flow cytometrists, the editors expect this authoritative up-to-date collection to prove useful to investigators in all areas of the biological and biomedical sciences who are new to the subject. The introductory chapter provides an eloquent synopsis of the principles and diverse uses of flow cytometry, beginning with a historical perspective and ending with a view to the future. Chapters 2–22 contain step-by-step protocols of highly practical and state-of-the-art techniques. Detailed instructions and helpful tips on experimental design, as well as selection of reagents and data analysis tools, will allow researchers to readily carry out flow cytometric investigations ranging from traditional phenotypic characterizations to emerging genomics and proteomics applications. Complementing these instructive protocols is a chapter that provides a preview of the next generation of solid-state lasers, and one that describes a rapid means to validate containment of infectious aerosols generated during high-speed sorting (Chapters 23–24). An elegant new color-based “cell gating” strategy that promises to simplify the analysis and visualization of complex multiparameter data is introduced in this volume. The sophistication of multiparameter flow cytometry is best demonstrated in function-based studies where molecular processes can be examined at the single cell level. This is beautifully illustrated by a novel technique that involves measurement of intracellular kinase signaling cascades using highly specific antibodies that differentiate between the phosphorylated and nonphosphorylated states of proteins. Combined with immunophenotyping, discrete biochemical signaling events in individual cells within

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heterogeneous populations can be deciphered. Other protocols are concerned with the characterization of T-cell subsets: intracellular cytokine staining can be used to quantify rare populations of antigen-specific T cells; cell tracking dyes can be combined with tetramer and cytokine staining to determine the frequency of antigen-specific - cell precursors destined to proliferate; and the cytolytic function of antigen-specific cytotoxic T lymphocytes can be assessed by a nonradioactive assay that monitors caspase activation in target cells, including primary cells of different lineages. Also described is a multidimensional approach to analyzing apoptosis that involves simultaneous analysis of caspase activation, annexin V binding to “flipped” phosphatidylserine residues, and membrane permeability to DNA binding dyes. Investigators planning to enter the stem cell arena will be introduced to several techniques for the detection of candidate stem cells. Two methods exploit the ability of hematopoietic stem cells to efflux the vital dyes Hoechst 33342 and rhodamine 123. Because these methods obviate the necessity to identify cell surface antigens, they are widely applicable to other types of stem cells that may lack well-defined phenotypes. A third method can be used to investigate the role of the CD34 surface antigen in the biology of human hematopoietic stem cells. The ability to readily introduce genes into primary cells, such as hematopoietic stem cells, has facilitated studies of cell fate. The green fluorescent protein (GFP) from jellyfish and GFP-like proteins from corals have become commonly used markers for this purpose. Unlike other bioluminescent reporters, fluorescence of GFP and GFP-related proteins does not require exogenous substrates or cofactors. Several schemes for simultaneous detection of multiple fluorescent proteins are presented. Cell isolation using the fluorescence-activated cell sorter (FACS) is an immensely powerful separation technique. The integration of FACS with microarray profiling will accelerate analysis of global gene expression within different cell types in complex tissues and organs. This recent development is discussed in one chapter in which practical details on microarray fabrication and hybridization are described. Also included are some innovative procedures for monitoring the interaction of biomolecules in living cells. Fluorescence resonance energy transfer (FRET) utilizing two spectral variants of GFP can be used to determine molecular association of proteins. Fusion of the proteins of interest to the GFP variants expands the horizon of FRET applications, which were previously limited by the availability of appropriate antibody pairs that would permit FRET to occur. Two new methods for discovering novel protein interactions are provided that take advantage of the high-throughput capability of FACS. The mammalian protein–protein interaction trap (MAPPIT) is a twohybrid assay used to screen complex cDNA libraries for new protein interaction

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partners. The second method allows rapid isolation of antigen-specific clones by flow cytometric screening of yeast surface display libraries. By displaying a library of single chain fragment variable antibodies (scFv) on the surface of yeast cells, the affinity of a clone can be characterized without the need for subcloning, expression, or purification of the scFv, and isolation of the highest affinity clones can be readily achieved by sorting. In other chapters, both basic and clinical scientists will find useful protocols for cell cycle analysis of asynchronous populations, and for the determination of DNA ploidy, RNA content, and the proliferative status of tumor cells. Also presented are a FRET-based assay to monitor HIV-1 virion fusion in primary T lymphocytes, which can be adapted to study fusion mediated by envelope proteins from other viruses, and an in situ flow cytometric assay (flow-FISH) for assessment of changes in telomere length during aging and malignant transformation, which is an alternative to the more laborious terminalrestriction-fragment Southern blotting methodology. Mounting interest in studying microorganisms parallels improved detection sensitivity of flow cytometers and development of microbespecific methodologies. The chapter on multiparameter flow cytometry of bacteria provides reliable methods for assessment of the physiologic states of Gram-negative or Gram-positive organisms. Burgeoning application of multiparameter flow cytometry to microbial analyses is anticipated. We would like to thank John Walker for inviting us to participate in this exciting endeavor and for his expert editorial assistance. We are especially grateful to all of the contributors for their enthusiasm. Their willingness to share their latest findings exemplifies the spirit of cooperation that is pervasive in the flow cytometry community. Teresa S. Hawley Robert G. Hawley

Contents Preface .............................................................................................................. v Contributors ..................................................................................................... xi 1 Flow Cytometry: An Introduction Alice L. Givan ....................................................................................... 1 2 Multiparameter Flow Cytometry of Bacteria Howard M. Shapiro and Gerhard Nebe-von-Caron ........................... 33 3 Multiparameter Data Acquisition and Analysis of Leukocytes Carleton C. Stewart and Sigrid J. Stewart .......................................... 45 4 Flow Cytometric Analysis of Kinase Signaling Cascades Omar D. Perez, Peter O. Krutzik, and Garry P. Nolan ...................... 67 5 Cytokine Flow Cytometry Holden T. Maecker ............................................................................. 95 6 Use of Cell-Tracking Dyes to Determine Proliferation Precursor Frequencies of Antigen-Specific T Cells Alice L. Givan, Jan L. Fisher, Mary G. Waugh, Nadège Bercovici, and Paul K. Wallace...................................................................... 109 7 Assessment of Lymphocyte-Mediated Cytotoxicity Using Flow Cytometry Luzheng Liu, Beverly Z. Packard, Martin J. Brown, Akira Komoriya, and Mark B. Feinberg ........................................ 125 8 Multiparametric Analysis of Apoptosis by Flow and Image Cytometry William G. Telford, Akira Komoriya, and Beverly Z. Packard ......... 141 9 Detection and Enrichment of Hematopoietic Stem Cells by Side Population Phenotype Shannon S. Eaker, Teresa S. Hawley, Ali Ramezani, and Robert G. Hawley .................................................................. 161 10 Hematopoietic Stem Cell Characterization by Hoechst 33342 and Rhodamine 123 Staining Ivan Bertoncello and Brenda Williams ............................................. 181 11 Phenotypic and Functional Analyses of CD34NEG Hematopoietic Precursors From Mobilized Peripheral Blood Douglas C. Dooley and Barbara K. Oppenlander ............................ 201 12 Multiparameter Flow Cytometry of Fluorescent Protein Reporters Teresa S. Hawley, Donald J. Herbert, Shannon S. Eaker, and Robert G. Hawley .................................................................. 219

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Contents 13 Analysis of Fluorescent Protein Expressing Cells by Flow Cytometry Steven C. Pruitt, Lawrence M. Mielnicki, and Carleton C. Stewart ............................................................... 239 14 Integrative Flow Cytometric and Microarray Approaches for Use in Transcriptional Profiling David W. Galbraith, Rangasamy Elumalai, and Fang Cheng Gong ..... 259 15 Flow Cytometric Analysis of Fluorescence Resonance Energy Transfer: A Tool for High-Throughput Screening of Molecular Interactions in Living Cells Francis Ka-Ming Chan and Kevin L. Holmes .................................... 281 16 Design of a Fluorescence-Activated Cell Sorting-Based Mammalian Protein–Protein Interaction Trap Sam Lievens, José Van der Heyden, Els Vertenten, Jean Plum, Joël Vandekerckhove, and Jan Tavernier ..................................... 293 17 Flow Cytometric Screening of Yeast Surface Display Libraries Michael Feldhaus and Robert Siegel ................................................. 311 18 Fluorescence Resonance Energy Transfer-Based HIV-1 Virion Fusion Assay Marielle Cavrois, Jason Neidleman, Martin Bigos, and Warner C. Greene ................................................................. 333 19 Cell-Cycle Analysis of Asynchronous Populations Michael G. Ormerod ........................................................................ 20 Solid Tumor DNA Content Analysis Adel K. El-Naggar and Philippe Vielh ............................................... 21 Concurrent Flow Cytometric Analysis of DNA and RNA Adel K. El-Naggar .............................................................................. 22 Telomere Length Measurement by Fluorescence In Situ Hybridization and Flow Cytometry Veena Kapoor and William G. Telford ............................................. 23 Small Lasers in Flow Cytometry William G. Telford ............................................................................ 24 Viable Infectious Cell Sorting in a BSL-3 Facility Stephen P. Perfetto, David R. Ambrozak, Mario Roederer, and Richard A. Koup .....................................................................

345 355 371

385 399

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Index ............................................................................................................ 425

Contributors DAVID R. AMBROZAK • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD NADÈGE BERCOVICI • IDM (Immuno-Designed Molecules), Paris, France IVAN BERTONCELLO • Stem Cell Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia MARTIN BIGOS • Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA MARTIN J. BROWN • OncoImmunin, Inc., Gaithersburg, MD MARIELLE CAVROIS • Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA FRANCIS KA-MING CHAN • Department of Pathology, University of Massachusetts Medical School, Worcester, MA DOUGLAS C. DOOLEY • Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR SHANNON S. EAKER • Healthspex, Inc., Knoxville, TN ADEL K. EL-NAGGAR • Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX RANGASAMY ELUMALAI • Department of Plant Sciences, University of Arizona, Tucson, AZ MARK B. FEINBERG • Departments of Medicine and Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA MICHAEL FELDHAUS • Battelle/Pacific Northwest National Laboratory, Richland, WA JAN L. FISHER • Department of Medicine, Dartmouth Medical School, Lebanon, NH DAVID W. GALBRAITH • Department of Plant Sciences, University of Arizona, Tucson, AZ ALICE L. GIVAN • Englert Cell Analysis Laboratory and Department of Physiology, Dartmouth Medical School, Lebanon, NH FANG CHENG GONG • Department of Plant Sciences, University of Arizona, Tucson, AZ WARNER C. GREENE • Gladstone Institute of Virology and Immunology and Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco, CA

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ROBERT G. HAWLEY • Hematopoiesis Department and Blood and Cell Therapy Development, Holland Laboratory, American Red Cross, Rockville, MD and Department of Anatomy and Cell Biology, The George Washington University, Washington, DC TERESA S. HAWLEY • Flow Cytometry Facility and Hematopoiesis Department, Holland Laboratory, American Red Cross, Rockville, MD DONALD J. HERBERT • Verity Software House Inc., Topsham, ME KEVIN L. HOLMES • Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD VEENA KAPOOR • Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD AKIRA KOMORIYA • OncoImmunin Inc., Gaithersburg, MD RICHARD A. KOUP • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD PETER O. KRUTZIK • The Baxter Laboratory for Genetic Pharmacology, Stanford University School of Medicine, Stanford, CA SAM LIEVENS • Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium LUZHENG LIU • Harvard Skin Disease Research Center, Boston, MA HOLDEN T. MAECKER • Immunocytometry Systems, BD Biosciences, San Jose, CA LAWRENCE M. MIELNICKI • Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY GERHARD NEBE-VON-CARON • Unipath Ltd., Bedford, UK JASON NEIDLEMAN • Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA GARRY P. NOLAN • The Baxter Laboratory for Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA BARBARA K. OPPENLANDER • Forest Grove, OR MICHAEL G. ORMEROD • Reigate, UK BEVERLY Z. PACKARD • OncoImmunin Inc., Gaithersburg, MD OMAR D. PEREZ • The Baxter Laboratory for Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA STEPHEN P. PERFETTO • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD JEAN PLUM • Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University Hospital, Ghent University, Ghent, Belgium

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STEVEN C. PRUITT • Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY ALI RAMEZANI • Hematopoiesis Department, Holland Laboratory, American Red Cross, Rockville, MD MARIO ROEDERER • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD HOWARD M. SHAPIRO • The Center for Microbial Cytometry and Howard M. Shapiro, MD, PC, West Newton, MA ROBERT SIEGEL • Battelle/Pacific Northwest National Laboratory, Richland, WA CARLETON C. STEWART • Laboratory of Flow Cytometry, Roswell Park Cancer Institute, Buffalo, NY SIGRID J. STEWART • Laboratory of Flow Cytometry, Roswell Park Cancer Institute, Buffalo, NY JAN TAVERNIER • Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium WILLIAM G. TELFORD • Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD JOËL VANDEKERCKHOVE • Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium JOSÉ VAN DER HEYDEN • Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium ELS VERTENTEN • Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium PHILIPPE VIELH • Service de Cytopathologie et Cytométrie Clinique, Institut Curie, Paris, France PAUL K. WALLACE • Flow Cytometry Resource, Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY MARY G. WAUGH • Department of Medicine, Dartmouth Medical School, Lebanon, NH BRENDA WILLIAMS • Stem Cell Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia

1 Flow Cytometry An Introduction Alice L. Givan Summary A flow cytometer is an instrument that illuminates cells (or other particles) as they flow individually in front of a light source and then detects and correlates the signals from those cells that result from the illumination. In this chapter, each of the aspects of that definition will be described: the characteristics of cells suitable for flow cytometry, methods to illuminate cells, the use of fluidics to guide the cells individually past the illuminating beam, the types of signals emitted by the cells and the detection of those signals, the conversion of light signals to digital data, and the use of computers to correlate and analyze the data after they are stored in a data file. The final section of the chapter will discuss the use of a flow cytometer to sort cells. This chapter can be read as a brief, self-contained survey. It can also be read as a gateway with signposts into the field. Other chapters in this book will provide more details, more references, and even some controversy about specific topics.

Key Words Flow cytometry, fluidics, fluorescence, laser.

1. Introduction An introductory chapter on flow cytometry must first confront the difficulty of defining a flow cytometer. The instrument described by Andrew Moldavan in 1934 (1) is generally acknowledged to be an early prototype. Although it may never have been built, in design it looked like a microscope but provided a capillary tube on the stage so that cells could be individually illuminated as they flowed in single file in front of the light emitted through the objective. The signals coming from the cells could then be analyzed by a photodetector attached in the position of the microscope eyepiece. Following work by CoulFrom: Methods in Molecular Biology: Flow Cytometry Protocols, 2nd ed. Edited by: T. S. Hawley and R. G. Hawley © Humana Press Inc., Totowa, NJ

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ter and others in the next decades to develop instruments to count particles in suspension (see refs. 2–5), a design was implemented by Kamentsky and Melamed in 1965 and 1967 (6,7) to produce a microscope-based flow cytometer for detecting light signals distinguishing the abnormal cells in a cervical sample. In the years after publication of the Kamentsky papers, work by Fulwyler, Dittrich and Göhde, Van Dilla, and Herzenberg (see refs. 8–11) led to significant changes in overall design, resulting in a cytometer that was largely similar to today’s cytometers. Like today’s cytometers, a flow cytometer in 1969 did not resemble a microscope in any way but was still based on Moldavan’s prototype and on the Kamentsky instrument in that it illuminated cells as they progressed in single file in front of a beam of light and it used photodetectors to detect the signals that came from the cells (see Shapiro [12] and Melamed [13,14] for more complete discussions of this historical development). Even today, our definition of a flow cytometer involves an instrument that illuminates cells as they flow individually in front of a light source and then detects and correlates the signals from those cells that result from the illumination. In this chapter, each of the aspects in that definition are described: the cells, methods to illuminate the cells, the use of fluidics to make sure that the cells flow individually past the illuminating beam, the use of detectors to measure the signals coming from the cells, and the use of computers to correlate the signals after they are stored in data files. As an introduction, this chapter can be read as a brief survey; it can also be read as a gateway with signposts into the field. Other chapters in this book (and in other books [e.g., refs. 12,15–24) provide more details, more references, and even some controversy concerning specific topics. 2. Cells (or Particles or Events) Before discussing “cells,” we need to qualify even that basic word. “Cytometer” is derived from two Greek words, “κντοζ”, meaning container, receptacle, or body (taken in modern formations to mean cell), and “μετρον”, meaning measure. Cytometers today, however, often measure things other than cells. “Particle” can be used as a more general term for any of the objects flowing through a flow cytometer. “Event” is a term that is used to indicate anything that has been interpreted by the instrument, correctly or incorrectly, to be a single particle. There are subtleties here; for example, if the cytometer is not quick enough, two particles close together may actually be detected as one event. Because most of the particles sent through cytometers and detected as events are, in fact, single cells, those words are used here somewhat interchangeably. Because flow cytometry is a technique for the analysis of individual particles, a flow cytometrist must begin by obtaining a suspension of particles. Historically, the particles analyzed by flow cytometry were often cells from the

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blood; these are ideally suited for this technique because they exist as single cells and require no manipulation before cytometric analysis. Cultured cells or cell lines have also been suitable, although adherent cells require some treatment to remove them from the surface on which they are grown. More recently, bacteria (25,26), sperm (27,28), and plankton (29) have been analyzed. Flow techniques have also been used to analyze individual particles that are not cells at all (e.g., viruses [30], nuclei [31], chromosomes [32], DNA fragments [33], and latex beads [34]). In addition, cells that do not occur as single particles can be made suitable for flow cytometric analysis by the use of mechanical disruption or enzymatic digestion; tissues can be disaggregated into individual cells and these can be run through a flow cytometer. The advantage of a method that analyzes single cells is that cells can be scanned at a rapid rate (500 to >5000 per second) and the individual characteristics of a large number of cells can be enumerated, correlated, and summarized. The disadvantage of a singlecell technique is that cells that do not occur as individual particles will need to be disaggregated; when tissues are disaggregated for analysis, some of the characteristics of the individual cells can be altered and all information about tissue architecture and cell distribution is lost. In flow cytometry, because particles flow in a narrow stream in front of a narrow beam of light, there are size restrictions. In general, cells or particles must fall between approx 1 μm and approx 30 μm in diameter. Special cytometers may have the increased sensitivity to handle smaller particles (such as DNA fragments [33] or small bacteria [35]) or may have the generous fluidics to handle larger particles (such as plant cells [36]). But ordinary cytometers will, on the one hand, not be sensitive enough to detect signals from very small particles and will, on the other hand, become obstructed with very large particles. Particles for flow cytometry should be suspended in buffer at a concentration of about 5 × 105 to 5 × 106/mL. In this suspension, they will flow through the cytometer mostly one by one. The light emitted from each particle will be detected and stored in a data file for subsequent analysis. In terms of the emitted light, particles will scatter light and this scattered light can be detected. Some of the emitted light is not scattered light, but is fluorescence. Many particles (notably phytoplankton) have natural background (auto-) fluorescence and this can be detected by the cytometer. In most cases, particles without intrinsically interesting autofluorescence will have been stained with fluorescent dyes during preparation to make nonfluorescent compounds “visible” to the cytometer. A fluorescent dye is one that absorbs light of certain specific colors and then emits light of a different color (usually of a longer wavelength). The fluorescent dyes may be conjugated to antibodies and, in this case, the fluorescence of a cell will be a readout for the amount of protein/antigen (on the cell surface or in the cytoplasm or nucleus) to which the antibody has bound.

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Some fluorochrome-conjugated molecules can be used to indicate apoptosis (37). Alternatively, the dye itself may fluoresce when it is bound to a cellular component. Staining with DNA-sensitive fluorochromes can be used, for example, to look at multiploidy in mixtures of malignant and normal cells (31); in conjunction with mathematical algorithms, to study the proportion of cells in different stages of the cell cycle (38); and in restriction-enzyme-digested material, to type bacteria according to the size of their fragmented DNA (39). There are other fluorochromes that fluoresce differently in relation to the concentration of calcium ions (40) or protons (41,42) in the cytoplasm or to the potential gradient across a cell or organelle membrane (43). In these cases, the fluorescence of the cell may indicate the response of that cell to stimulation. Other dyes can be used to stain cells in such a way that the dye is partitioned between daughter cells on cell division; the fluorescence intensity of the cells will reveal the number of divisions that have occurred (44). Chapters in this book provide detailed information about fluorochromes and their use. In addition, the Molecular Probes (Eugene, OR) handbook by Richard Haugland is an excellent, if occasionally overwhelming, source of information about fluorescent molecules. The important thing to know about the use of fluorescent dyes for staining cells is that the dyes themselves need to be appropriate to the cytometer. This requires knowledge of the wavelength of the illuminating light, knowledge of the wavelength specificities of the filters in front of the instrument’s photodetectors, and knowledge of the absorption and emission characteristics of the dyes themselves. The fluorochromes used to stain cells must be able to absorb the particular wavelength of the illuminating light and the detectors must have appropriate filters to detect the fluorescence emitted. For the purposes of this introductory chapter, we now assume that we have particles that are individually suspended in medium at a concentration of about 1 million/mL and that they have been stained with (or naturally contain) fluorescent molecules with appropriate wavelength characteristics. 3. Illumination In most flow cytometers, fluorescent cells are illuminated with the light from a laser. Lasers are useful because they provide intense light in a narrow beam. Particles in a stream of fluid can move through this light beam rapidly; under ideal circumstances, only one particle will be illuminated at a time, and the illumination is bright enough to produce scattered light or fluorescence of detectable intensity. Lasers in today’s cytometers are either gas lasers (e.g., argon ion lasers or helium–neon lasers) or solid-state lasers (e.g., red or green diode lasers or the relatively new blue and violet lasers). In all cases, light of specific wavelengths

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Table 1 Common Types of Lasers in Current Use Laser Argon ion Red helium–neon (He–Ne) Green helium neon (He–Ne) Krypton ion Violet diode Blue solid state Red diode

Emission Wavelength(s) (nm) Usually 488, 514, UV(351/364) 633 543 Usually 568, 647 408 488 635

is generated (see Table 1). The wavelengths of the light from a given laser are defined and inflexible, based on the characteristics of the lasing medium. The most common laser found on the optical benches of flow cytometers today is an argon ion laser; it was chosen for early flow cytometers because it provides turquoise light (488 nm) that is absorbed efficiently by fluorescein, a fluorochrome that had long been used for fluorescence microscopy. Argon ion lasers can also produce green light (at 514 nm), ultraviolet light (at 351 and 364 nm), and a few other colors of light at low intensity. Some cytometers will use only 488-nm light from an argon ion laser; other cytometers may permit selection of several of these argon ion wavelengths from the laser. Whereas the early flow cytometers used a single argon ion laser at 488 nm to excite the fluorescence from fluorescein (and later to include, among many possible dyes, phycoerythrin, propidium iodide, peridinin chlorophyll protein [PerCP], and various tandem transfer dyes—all of which absorb 488-nm light), there was an increasing demand for fluorochromes with different emission spectra so that cells could be stained for many characteristics at once and the fluorescence from the different fluorochromes distinguished by color. This led to the requirement for illumination light of different wavelengths and therefore for an increasing number of lasers on the optical bench. Current research flow cytometers may include, for example, two or three lasers from those listed in Table 1. Flow cytometers with more than one laser focus the beam from each laser at a different spot along the stream of flowing cells (Fig. 1). Each cell passes through each laser beam in turn. In this way, the scatter and fluorescence signals elicited from the cells by each of the different lasers will arrive at the photodetectors in a spatially or temporally defined sequence. Thus, the signals from the cells can be associated with a particular excitation wavelength. All the information that a flow cytometer reveals about a cell comes from the period of time that the cell is within the laser beam. That period begins at the

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Fig. 1. Cells flowing past laser beam analysis points (in a three-laser cytometer). Beams with elliptical cross-sectional profiles allow cells to pass into and out of the beam quickly, mainly avoiding the coincidence of two cells in the laser beam at one time (but see the coincidence event in the first analysis point). In addition, an elliptical laser beam provides more uniform illumination if cells stray from the bright center of the beam.

time that the leading edge of the cell enters the laser beam and continues until the time that the trailing edge of the cell leaves the laser beam. The place where the laser beam intersects the stream of flowing cells is called the “interrogation point,” the “analysis point,” or the “observation point.” If there is more than one laser, there will be several analysis points. In a standard flow cytometer, the laser beam(s) will have an elliptical cross-sectional area, brightest in the center and measuring approx 10–20 × 60 μm to the edges. The height of the laser beam (10–20 μm) marks the height of the analysis point and the dimension through which each cell will pass. In commercial and research cytometers, cells will flow through each analysis point at a velocity of 5–50 m/s. They will,

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Fig. 2. The probability of a flow cytometric “event” actually resulting from more than one cell coinciding in the analysis point. For this model, the laser beam was considered to be 30 μm high and the stream flowing at 10 meters per second. (Reprinted with permission of John Wiley & Sons. Copyright 2001 from Givan, A. L. [2001] Flow Cytometry: First Principles, 2nd edit. Wiley-Liss, New York.)

therefore, spend approx 0.2–4 μs in the laser beam. Because fluorochromes typically absorb light and then emit that light in a time frame of several nanoseconds, a fluorochrome on a cell will absorb and then emit light approximately a thousand times while the cell is within each analysis point. 4. Fluidics: Cells Through the Laser Beam(s) In flow cytometry, as opposed to traditional microscopy, particles flow. In other words, the particles need to be suspended in fluid and each particle is then analyzed over the brief and defined period of time that it is being illuminated as it passes through the analysis point. This means that many cells can be analyzed and statistical information about large populations of cells can be obtained in a short period of time. The downside of this flow of single cells, as mentioned previously, is that the particles need to be separate and in suspension. But even nominal single-cell suspensions contain cells in clumps if the cells tend to aggregate; or there may be cells in “pseudo-clumps” if they are in a concentrated suspension and, with some probability, coincide with other cells in the analysis point of the cytometer. Even in suspensions of low cell concentration, there is always some probability that coincidence events will occur (Fig. 2). The fluidics in a cytometer are designed to decrease the probability that multiple cells will coincide in the analysis point; in addition, the fluidics must facilitate similar illumination of each cell, must be constructed so as to avoid obstruction of the flow tubing, and must do all of this with cells flowing in and out of the analysis point as rapidly as possible (consistent with the production of sufficiently intense scattered and fluorescent light for sensitive detection).

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One way to confine cells to a narrow path through the uniformly bright center of a laser beam would be to use an optically clear chamber with a very narrow diameter or, alternatively, to force the cells through the beam from a nozzle with a very narrow orifice. The problem with pushing cells from a narrow orifice or through a narrow chamber is that the cells, if large or aggregated, tend to clog the pathway. The hydrodynamics required to bring about focussed flow without clogging is based on principles that date back to work by Crosland-Taylor in 1953 (45). He noted that “attempts to count small particles suspended in fluid flowing through a tube have not hitherto been very successful. With particles such as red blood cells the experimenter must choose between a wide tube that allows particles to pass two or more abreast across a particular section, or a narrow tube that makes microscopical observation of the contents of the tube difficult due to the different refractive indices of the tube and the suspending fluid. In addition, narrow tubes tend to block easily.” Crosland-Taylor’s strategy for confining cells in a focussed, narrow flow stream but preventing blockage through a narrow chamber or orifice involved injecting the cell suspension into the center of a wide, rapidly flowing stream (the sheath stream), where, according to hydrodynamic principles, the cells will remain confined to a narrow core at the center of the wider stream (46). This so-called hydrodynamic focussing results in coaxial flow (a narrow stream of cells flowing in a core within a wider sheath stream); it was first applied to cytometry by Crosland-Taylor, who realized that this was a way to confine cells to a precise position without requiring a narrow stream that was susceptible to obstruction. The “flow cell” is the site in the cytometer where the sample stream is injected into the sheath stream (Figs. 3 and 4). After joining the sheath stream, the velocity of the cell suspension (in meters per second) either increases or decreases so that it becomes equal to the velocity of the sheath stream. The result is that the cross-sectional diameter of the core stream containing the cells will either increase or decrease to bring about this change in the velocity of flow while maintaining the same sample volume flow rate (in milliliters per second). The injection rate of the cell suspension will therefore directly affect the width of the core stream and the stringency by which cells are confined to the center of the illumination beam. After use of hydrodynamic focusing to align the flow of the cells within a wide sheath stream so that blockage is infrequent, there is still a requirement for rapid analysis, for better confining of the flow of cells to the very bright center of the laser beam, and for the avoidance of coincidence of multiple cells in the analysis point. These characteristics are provided by the design of the flow cell (cf. 47). Some cytometers illuminate the stream of cells within an optically clear region of the flow cell (as in a cuvet). Other systems use flow cells where the light beam intersects the fluid stream after it emerges from the

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Fig. 3. The fluidics system of a flow cytometer, with air pressure pushing both the sample with suspended cells and the sheath fluid into the flow cell. (Reprinted with permission of John Wiley & Sons. Copyright 2001 from Givan, A. L. [2001] Flow Cytometry: First Principles, 2nd edit. Wiley-Liss, New York; and also from Givan, A. L. [2001] Principles of flow cytometry: an overview, in Cytometry, 3rd edit. [Darzynkiewicz, Z., et al., eds.], Academic Press, San Diego, CA, pp. 415–444.)

flow cell through an orifice (“jet-in-air”). In all cases, the flow cell increases the velocity of the stream by having an exit orifice diameter that is narrower than the diameter at the entrance. The differences in diameter are usually between 10- and 40-fold, bringing about an increase in velocity equal to 100- to 1600fold (47). As the entire stream (with the cell suspension in the core of the sheath stream) progresses toward the exit of the flow cell, it narrows in diameter and increases in velocity. With this narrowing of diameter and increasing of velocity, the path of the cells becomes tightly confined to the center of the laser beam so that all cells are illuminated similarly and the cells move through the laser beam rapidly. In addition, cells are spread out at greater distances from each other in the now very narrow stream and are therefore less likely to coincide in the analysis point. In summary, with regard to the fluidics of the flow cytometer, the hydrodynamic focussing of a core stream of cells within a wider sheath stream facili-

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Fig. 4. A flow cell, with the sample suspension injected into the sheath fluid and forming a central core in the sheath stream. The small diameter of the flow cell at its exit orifice causes the sheath stream and sample core to narrow so that cells flow rapidly and are separated from each other and less likely to coincide in the analysis point.

tates the alignment of cells in the center of the laser beam without the clogging problems associated with narrow tubing and orifices. In addition, the flow cell itself increases the velocity of the stream; as well as increasing the rate at which cells are analyzed, this increased velocity also narrows the core stream to align it more precisely in the uniformly bright center of the laser beam and, at the same time, increases the distance between cells in the stream so that coincidence events in the analysis point are less frequent. 5. Signals From Cells Lenses around the analysis point collect the light coming from cells as a result of their illumination by the laser(s). Typically there are two lenses, one in the forward direction along the path of the laser beam and one at right angles (orthogonal) to this direction (Fig. 5). These lenses collect the light (the signals) given off by each cell as it passes through the analysis point. The lens in the forward direction focusses light onto a photodiode. Across the front of this forward lens is a blocker (or “obscuration”) bar, approx 1 mm wide, positioned so as to block the laser beam itself as it passes through the stream. Only light

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Fig. 5. The analysis point of a flow cytometer, with the laser beam, the sheath stream, and the lenses for collection of forward scatter and side scatter/fluorescence all at orthogonal angles to each other.

from the laser that has been refracted or scattered as it goes through a particle in the stream will be diverted enough from its original direction to avoid the obscuration bar and strike the forward-positioned lens and the photodiode behind it. Light striking this forward scatter photodetector is therefore light that has been bent to small angles by the cell: the three-dimensional range of angles collected by this photodiode falls between those obscured by the bar and those lost at the limits of the outer diameter of the lens. The light striking this photodetector is called forward scatter light (“fsc”) or forward angle light scatter (“fals”). Although precisely defined in terms of the optics of light collection for any given cytometer, forward scatter light is not well defined in terms of the biology or chemistry of the cell that generates this light. A cell with a large cross-sectional area will refract a large amount of light onto the photodetector. But a large cell with a refractive index quite close to that of the medium (e.g., a dead cell with a permeable outer membrane) will refract light less than a similarly large cell with a refractive index quite different from that of the medium. Because of the rough relationship between the amount of light refracted past the bar and the size of the particle, the forward scattered light signal is sometimes (misleadingly) referred to as a “volume” signal. This term belies its complexity (48).

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The lens at right angles to the direction of the laser beam collects light that has been scattered to wide angles from the original direction. Light collected by this lens is defined by the diameter of the lens and its distance from the analysis point and is called side scatter light (“ssc”) or 90° light scatter. Laser light is scattered to these angles primarily by irregularities or texture in the surface or cytoplasm of the cell. Granulocytes with irregular nuclei scatter more light to the side than do lymphocytes with spherical nuclei. Similarly, more side scatter light is produced by fibroblasts than by monocytes. The signals that have been described so far (forward scatter and side scatter) are signals of the same color as the laser beam striking the cell. In a single laser system, this is usually 488-nm light from an argon ion laser; in a system with two or more lasers, the scattered light is also usually 488 nm, because it is collected from the primary laser beam. As we have described, this scattered light provides information about the physical characteristics of the cell. In addition to this scattered light, the cell may also give off fluorescent light: fluorescent light is defined as light of a relatively long wavelength that is emitted when a molecule absorbs high energy light and then emits the energy from that light as photons of somewhat lower energy. Fluorescein absorbs 488-nm light and emits light of approx 530 nm. Phycoerythrin absorbs 488-nm light and emits light of approx 580 nm. Therefore, if a cell has been stained with antibodies of a particular specificity conjugated to fluorescein and with antibodies of different specificity conjugated to phycoerythrin and then the cell passes through a 488-nm laser beam, it will emit light of 530 nm and 580 nm. Some cells may also contain endogenous fluorescent molecules (such as chlorophyll or pyridine or flavin nucleotides). In addition, cells can be stained with other probes that fluoresce more or less depending on the DNA content of the cell or the calcium ion content of the cell, for example. In all these cases, the intensity of the fluorescent light coming from the cell is, to an arguable extent, related to the abundance of the antigen or the DNA or the endogenous molecule or the calcium ion concentration of the cell. Measuring the intensity of the fluorescent light will give, then, some indication of the phenotype or function of the cells flowing through the laser beam(s). Detecting fluorescent light is similar to detecting side-scatter light, but with the addition of wavelength-specific mirrors and filters (see ref. 49). These mirrors and filters are designed so that they transmit and reflect light of welldefined wavelengths. The light emitted to the side from an analysis point is focussed by the lens onto a series of dichroic mirrors and bandpass filters that partition this multicolor light, according to its color, onto a series of separate photomultiplier tubes (see Figs. 6 and 7). In a simple example, side scatter light (488 nm) is directed toward one photomultiplier tube (PMT); light of 530 nm is directed toward another PMT; light of 580 nm is directed toward

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Fig. 6. The use of wavelength-specific bandpass and longpass filters and dichroic mirrors to partition the light signal from cells to different photodetectors according to its color. In the system depicted here, there are five photodetectors; they detect forward scatter light, side scatter light, and fluorescence light in the green, orange, and red wavelength ranges. (Reprinted with permission of John Wiley & Sons, Inc. Copyright 2001 from Givan, A. L. [2001] Flow Cytometry: First Principles, 2nd edition. Wiley-Liss, New York.)

another PMT; and light >640 nm is directed toward another PMT (Fig. 6). In this example, the system will have four PMTs at the side, individually specific for turquoise, green, orange, or red light. Adding in the additional photodetector for forward scatter light, this instrument would be called a five-parameter flow cytometer. Flow cytometers today have, typically, anywhere from 3 to 15 photodetectors and thus are capable of detecting and recording the intensity of forward scatter light, side scatter light, and fluorescent light of 1–13 different colors. Because multiple excitation wavelengths are required to excite a large range of fluorochromes (distinguishable by their fluorescence emission wavelengths), high-parameter cytometers normally will have several lasers. The cells will pass, in turn, through each of the laser beams and the photodetectors will be arranged spatially so that some of the detectors will measure light excited by the first laser, some will measure light excited by the second laser, and so forth. The signals emitted by a cell as it passes through each laser beam are light pulses that occur over time, with a beginning, an end, a height, and an inte-

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Fig. 7. Arrangement of eight PMTs with their dichroic mirrors and bandpass filters to partition light from the analysis point. Light enters the octagon via a fiber and progresses toward PMT 1; at the dichroic mirror in front of PMT 1, light of some colors is transmitted and reaches PMT 1, but light of other colors is partitioned and reflected toward PMT 2. At the dichroic mirror in front of PMT 2, light of some colors is transmitted toward PMT 2, but light of other colors is reflected toward PMT 3. In this way, light progresses through the octagon, with specific colors directed toward specific photodetectors. This octagon system has been developed by Becton Dickinson (BD Biosciences, San Jose, CA); this figure is a modification of graphics from that company.

grated area. On traditional cytometers, the signal is “summarized” either by the height of the signal (related to the maximum amount of light given off by the cell at any time as it passes through the laser beam) or by the integrated area of the signal (related to the total light given off by the cell as it passes through the laser beam). Some newer cytometers analyze the signal repeatedly (10 million times per second) during the passage of the cell through the beam and those multiple numbers are then processed to give a peak height or integrated area readout or can be used to describe the pattern of light as it is related to the structure of the cell along its longitudinal axis. With these options, there will be one or more values that are derived from each photodetector for each cell. In a simple case, for example, only the integrated (area) fluorescence

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Fig. 8. The graphing of flow cytometric signals from fluorescent beads of five different intensities. The signals in the upper graph were acquired on an analog cytometer with linear amplification; the intensity values reported by an analog-to-digital converter with 1024 channels have been plotted directly on the histogram axis. The two brightest beads are off scale (at the right-hand edge of the graph). The signals in the lower graph were acquired on an analog cytometer with logarithmic amplification; intensity values reported by the 1024-channel ADC can be plotted according to channel number, but are conventionally plotted according to the derived value of “relative intensity.” With logarithmic amplification, beads of all five intensities are “on scale.” (Reprinted from Givan, A. L. [2001] Principles of flow cytometry: an overview, in Cytometry, 3rd edition [Darzynkiewicz, Z., et al., eds.], Academic Press, San Diego, CA, pp. 415–444.)

detected by each photodetector will be used; the values stored for these integrated intensities from, for example, a five-photodetector system, will form the five-number flow cytometric description of each cell. A fifteen parameter system will have, in this simple example, a 15-number flow description for each cell. 6. From Signals to Data In a so-called “analog” or traditional cytometer, the current from each photodetector will be converted to a voltage, will be amplified, may be processed

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for ratio calculations or spectral cross-talk correction, and then, finally, will be digitized by an analog-to-digital converter (ADC) so that the final output numbers will have involved binning of the analog (continuous) amplified and processed values into (digital) channels. The amplification can be linear or logarithmic. If linear amplification is used, the intensity value is usually digitized and reported on a 10-bit or 1024-channel scale and is displayed on axes with linear values; the numbers on the axis scale are proportional to the light intensity (Fig. 8, upper graph). By contrast, if logarithmic amplifiers are used, the output voltage from the amplifier is proportional to the logarithm of the original light intensity; it will be digitized, again usually on a 1024-channel scale, and the digitized final number will be proportional to the log of the original light intensity. In this case, the usual display involves the conversion of the values to “relative intensity units” and the display of these on axes with a logarithmic scale (Fig. 8, bottom axis of lower graph). When logarithmic amplifiers are used, they divide the full scale into a certain number of decades: that is, the full scale will encompass three or four or more 10-fold increases; a four decade scale is common (that is, something at the top end of the scale will be 104 times brighter than something at the bottom end of the scale). It is important here to understand the reasons for choice of linear or logarithmic amplification. Linear amplification displays a limited range of intensities; logarithmic amplification, by contrast, will display a larger range of intensities (compare upper and lower graphs in Fig. 8). For this reason, linear amplifiers are conventionally used for measurements of DNA content—where the cells with the most DNA in a given analysis will generally have about twice the DNA content of the cells with the lowest DNA content. By contrast, cells that express proteins may have, after staining, 100 or 1000 times the brightness of cells that do not express those proteins; logarithmic amplification allows the display of both the positive and negative cells on the same graph. Although the terminology is confusing (because all cytometers report, in the end, digitized channel numbers), some newer flow systems are referred to as “digital systems” because the current from the photodetectors is converted to a voltage and then digitized immediately without prior amplification and processing. There are advantages to this early digitization that relate to time and to the elimination of some less than perfect electronic components (see refs. 12,50). By using high-resolution analog-to-digital converters, the intensity values from the signal (possibly sampled at 10 MHz) can be reported on a 14-bit or 16,384-channel scale. The reported digitized numbers can then be processed to describe the integrated area, the height, or the width of the signal, where the integrated area, in particular, is usually most closely proportional to the intensity of the original light signal. Because the numbers are reported to high resolution, they can then be plotted on either linear or logarithmic axes. These

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Fig. 9. A flow cytometric data file is a list of cells in the order in which they passed through the analysis point. In this five-parameter file, each cell is described by five numbers for the signals from the forward scatter (fsc), side scatter (ssc), green fluorescence (fl.), orange fluorescence, and red fluorescence photodetectors.

high resolution ADCs obviate the need for logarithmic amplifiers, avoiding some of the problems that derive from their nonlinearity (see refs. 51–53). What we now have described is a system that detects light given off by a particle in the laser beam; the light is detected according to which laser has excited the fluorescence or scatter, according to the direction the light is emitted (forward or to the side), and according to its color. The intensity of the light striking each photodetector may be analyzed according to its peak height intensity, its integrated area (total) intensity, or according to the many numbers that describe the signal over time. The numbers derived from each photodetector can be recorded digitally or can be amplified either linearly or logarithmically before digitization. Each cell will then have a series of numbers describing it, and the data file contains the collection of numbers describing each cell that has been run through the cytometer during the acquisition of a

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particular sample (Fig. 9). If 10,000 cells have been run through the cytometer and it is a five-detector cytometer, there will be five numbers describing each cell (or ten, if, e.g., signal width and signal height are both recorded). If five parameters have been recorded for each cell, the data file will consist of a list of 50,000 numbers, describing in turn all the cells in the order in which they have passed through the laser beam. The data file structure will conform more or less to a published flow cytometry standard (FCS) format (54). 7. From Data to Information After the data about a group of cells are stored into a data file, all the remaining processes of flow cytometry are computing. Instrument vendors write software for the analysis of data acquired on their instruments; independent programmers write software for the analysis of data acquired on any instrument. Software packages vary in price, elegance, and sophistication, but they all perform some of the same functions: they all allow a display of the distribution of any one parameter value for the cells in the data file (in a histogram); they all allow a display of correlated data between any two parameters’ values (in a dot plot or contour plot or density plot) ; and they all allow the restriction of the display of information to certain cells in the data file (“gating”). A histogram (Fig. 10) is used to display the distribution of one parameter over the cells in the data file. With the data from a five-parameter flow cytometer, there will be five numbers describing each cell (e.g., the intensities of forward scatter, side scatter, green fluorescence, orange fluorescence, and red fluorescence). A histogram (really a bar graph, with fine resolution between categories so that the bars are not visible) can display the distribution of each of those five parameters (in five separate histograms), so that we can see whether the distribution for each parameter is unimodal or bimodal; what the average relative intensities are of the cells in the unimodal cluster or in the two bimodal clusters; what proportion of the cells have intensities brighter or duller than a certain value. Numbers can be derived from these histogram distributions; by using “markers” or “cursors” to delineate ranges of intensity, software can report the proportion of cells with intensities in each of the ranges. Because a flow data file provides several numbers (in the case of a fiveparameter flow cytometer, five numbers) describing each cell, plotting all the data on five separate histograms does not take advantage of the ability we have to reveal information about the correlation between parameters on a single-cell basis. For example, do the cells that fluoresce bright green also fluoresce orange or do they not fluoresce orange? For the display of correlated data, flow software provides the ability to plot dot plots or contour plots or density plots. Although these alternative two-dimensional plots have different advantages in

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Fig. 10. The five histograms derived from a five-parameter flow cytometric data file. The scatter and fluorescence distributions are plotted individually for all the cells in the file. Forward and side scatter were acquired with linear amplification and the integrated intensity values (“area”) are plotted according to the ADC channel number. The fluorescence signals were acquired with logarithmic amplification and their integrated intensity values are plotted according to the derived value of relative intensity.

terms of visual impact and graphical authenticity to the hard data, they all display two parameters at once and report the same quantitative analysis (Fig. 11). By using a two-dimensional plot, a scientist can see whether the cells that fluoresce green also fluoresce orange. Further, this information can be reported quantitatively, using markers to delineate intensity regions in two dimensions. These two-dimensional markers are called quadrants if they have been used to

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Fig. 11. A two-dimensional density plot, indicating the correlation of green and orange fluorescence for the cells in a data file. Quadrants divide the intensity distributions into regions for unstained (“double-negative”) cells, cells that are stained both green and orange (“double-positive cells”), and cells stained for each of the colors singly. In this example, it can be seen that most of the green-positive cells are not also orange-positive (that is, they are not double positive).

delineate so-called double-negative, single-positive (for one color), singlepositive (for the second color), and double-positive cells (Fig. 11). One of the unique aspects of flow cytometry is the possibility of “gating.” Gating is the term used for the designation of cells of interest within a data file for further analysis. It permits the analysis of subsets of cells from within a mixed population. It also provides a way to analyze cells in high levels of multiparameter space (55,56). Figure 12 shows an example of a mixed population of white blood cells that have been stained with fluorescent antibodies. Because the white blood cells of different types can be distinguished from each other by the separate clusters they form in a plot of forward scatter vs side scatter light, the fluorescence of the monocytes can be analyzed without interference from the fluorescence of the lymphocytes or neutrophils in the data file. Similarly, the neutrophils and lymphocytes can also be analyzed independently of the other populations of cells. The procedure for doing this involves drawing a “region” around the cluster of, for example, monocytes in the fsc vs ssc plot. That region defines a group of cells with particular characteristics in

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Fig. 12. A plot of forward vs side scatter for leukocytes from the peripheral blood indicates that regions can be drawn around cells with different scatter characteristics, marking lymphocytes, monocytes, and neutrophils. These regions can be used to define gates. The four plots of green vs orange fluorescence are either ungated displaying the fluorescence intensities of all the cells (upper right); or are gated on each of the three leukocyte populations, revealing that the three types of leukocytes stain differently with the orange and green antibodies.

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the way they scatter light. The region can then be used as a gate for subsequent analysis of the fluorescence of cells. A gated dot plot of, for example, green fluorescence vs orange fluorescence can display the fluorescence data from only the cells that fall into the “monocyte” region. Gates can be simple in this way. Or they can be more complex, facilitating the analysis of cells that have been stained with many reagents in different colors: for example, a gate could be a combination of many regions, defining cells with certain forward and side scatter characteristics, certain green fluorescence intensities, and certain orange fluorescence intensities. The final step in analysis could use a gate that combines all these regions and could then ask how the cells with bright forward scatter, medium side scatter, bright green intensity, and little or no orange intensity are distributed with regard to red fluorescence. 8. Sorting It might seem that flow cytometers would have developed first with the ability to detect many colors of fluorescence from particles or cells and that it then might have occurred to someone that it would be useful to separate cells with different fluorescent or scatter properties into separate test tubes for further culture, for RNA or DNA isolation, or for physiological analysis. The actual history, however, followed the opposite course. Early flow cytometers were developed to separate cells from each other (7,8,11). A cytometer was developed in 1965 by Mack Fulwyler at the Los Alamos National Laboratory to separate red blood cells with different scatter signals from each other to see if there were actually two separate classes of erythrocytes or, alternatively, if the scatter differences were artifactual based on the flattened disc shape of the cells. The latter turned out to be true—and the same instrument was then used to separate mouse from human erythrocytes and a large component from a population of mouse lymphoma cells (8). For several years, flow cytometers were thought of as instruments for separating cells (the acronym FACS stands for “fluorescence-activated cell sorter”). It was only slowly that these instruments began to be used primarily for the assaying of cells without separation. Modern cytometers most often do not even possess the capability of separating cells. Although many methods are available for separating/isolating subpopulations of cells from a mixed population (e.g., adherence to plastic, centrifugation, magnetic bead binding, complement depletion) and these methods are usually significantly more rapid than flow sorting, flow sorting may be the best separation technique available when cells differ from each other by the way they scatter light, by slight differences in antigen intensity, or by multiparameter criteria. Cells sorted by flow cytometry are routinely used for functional assays, for polymerase chain reaction (PCR) replication of cell-type specific DNA sequences, for artificial insemination by sperm bearing X or Y chromo-

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Fig. 13. Droplet formation for sorting. A vibrating flow cell causes the sheath stream to break up into drops at the breakoff point. Cells flowing in the stream are enclosed in drops and, in the example shown here, drops can be charged strongly or less strongly positive or negative, so that four different types of cells (as detected at the analysis point) can be sorted into four receiving containers.

somes, and for cloning of high-expressing transfected cells. In addition, sorted chromosomes are used for the generation of DNA libraries. The strategy for electronic flow sorting involves the modification of a nonsorting cytometer in three ways: the sheath stream is vibrated so that it breaks up into drops; the stream (now in drops) flows past two charged (high-voltage) plates; and the electronics of the instrument are modified so that the drops can be charged or not according to the characteristics of any contained cell, as detected at the analysis point (Fig. 13). In a sorting cytometer, cells flow through the analysis point where they are illuminated and their scatter and fluorescence sig-

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nals detected as in a nonsorting instrument. They then continue to flow downstream where, as the stream breaks up into drops, they become enclosed in individual drops. If the cells are far enough apart from each other in the stream, there will be very few cases in which there is more than one cell in each drop; there will be, by operator choice, cells in, on average, only every third or fifth or tenth drop—and there will be empty drops between the drops containing cells. The number of cells per drop (and the number of empty drops) will be determined by the number of cells flowing per second, by the vibration frequency that is creating the drops, and by the impact of the mathematics of a Poisson distribution, whereby cells are never perfectly distributed along the stream but can cluster with some probability (the Fifth Avenue bus phenomenon). A vibrating stream breaks up into drops according to the following equation v=fλ

which defines the fixed relationship between the velocity of the stream (v), the frequency of the drop generation vibration ( f ), and the distance between the drops (λ). Drop formation is stable when the distance between drops equals 4.5 times the diameter of the stream, so a given stream diameter (flow cell exit orifice) will determine the λ value. Rapid drop formation (high f ) is desirable because rapid drop formation allows rapid cell flow rate (without multiple cells in a drop). Therefore this condition is facilitated by using a high stream velocity and also a narrow stream diameter (but being aware that a narrow flow cell orifice gets clogged easily). Common conditions for sorting, with a 70-μm flow cell orifice, involve stream velocities of about 10 m/s and drop drive frequencies of about 32 kHz (meaning that cells flowing at 10,000 cells per second will be, on average, in every third drop). Conditions for so-called high speed sorting involve stream velocities of about 30 m/s and drop drive frequencies of 95 kHz (cells flowing at 30,000 cells/s will be, on average, in every third drop). Because drops break off from the vibrating stream at a distance from the fixed point of vibration, the stream of cells can be illuminated and the signals from the cells collected with little perturbation as long as the analysis point is relatively close to the point of vibration and far away from the point of drop formation. In a sorting cytometer, cells are illuminated close to the flow cell (or within an optically clear flow cell); their signals are collected, amplified, and digitized in ways similar to those in nonsorting cytometers. A sorting cytometer differs from a nonsorting cytometer because cells become enclosed in drops after they move down the stream. At points below the drop breakoff point, the stream will consist of a series of drops, all separate from each other, with some drops containing cells. The flow operator will have drawn sort regions around cells “of interest” according to their flow parameters. If a cell in the analysis point has been determined to be a cell of interest according to the sort regions,

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the drop containing that cell will be charged positively or negatively so that it will be deflected either to the left or right as it passes the positive and negative deflection plates. Modern cytometers have the ability to charge drops in four ways (strongly or weakly positive and strongly or weakly negative), so that four sort regions can be designated and four subpopulations of cells can be isolated from the original population. Collecting tubes are placed in position, one or two more or less at the left and one or two more or less at the right, and the deflected drops, containing the cells of interest, will be collected in the tubes. Uninteresting cells will be in uncharged drops; they will not be deflected out of the main stream and they will pass down the center and into the waste container. Sorted cells will be pure when only those drops containing the cells of interest are charged. This happens because the sort operator determines the length of time required for a cell to move from the analysis point to the position of its enclosure in a drop (at the drop “breakoff point” downstream); the stream is charged for a short period of time at exactly this time delay after a cell of interest has been detected. This drop delay time can be determined empirically, by testing different drop delay times on a test sort with beads. Alternatively, it can be measured using drop separation units (knowing the drop generation frequency, the reciprocal is equal to the number of seconds per drop; therefore, the distance between drops [which can be measured] has an equivalence in time units). Given the time that it takes between analysis of a cell in the laser beam and the enclosure of that cell into its own self-contained drop, the flow cytometer can be programmed to apply a charge to the stream for a short interval, starting at the time just before the cell of interest is about to detach from the main stream into the drop. If the charge is applied for a short interval, only one drop will be charged. If it is charged for a longer interval, then drops on either side of the selected drop can be charged (for security, in case the cell moves faster or slower than predicted). The charge on the stream can be positive or negative (or weakly or strongly positive or negative) and therefore the drops containing two or four mutually exclusive subsets of cells can be deflected into separate collection vessels. Cell sorting is validated by three characteristics: the efficiency of the sorting of the cells of interest from the original mixed population; the purity of those cells according to the selection criteria; and the time it has taken to obtain a given number of sorted cells (57). In most cytometers, purity is protected because drop charging is aborted when cells of the wrong phenotype are enclosed with cells of interest in a single drop. In this way, high cell flow rates will compromise the sorting efficiency but will not compromise purity until the cell flow rate is so fast that there is significant coincidence of multiple cells in the laser beam. As the cell flow rate increases (using cells at higher concen-

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Fig. 14. The efficiency and speed of sorting are affected by the flow rate of cells through the analysis point. Sorting at a high flow rate decreases the efficiency but increases the speed at which sorted cells are collected (until so many sorts are aborted as a result of multiple cells in drops that the sort rate begins to decline). The model from which these graphs were derived is from Robert Hoffman.

trations), the speed of sorting will increase until the number of aborted sorts gets so high that the actual speed of sorting of the desired cells starts to drop off (Fig. 14). Some sorting protocols will be designed to obtain rare cells: these sorts will be done at relatively low speed but with resulting high efficiency. Other protocols will start with buckets of cells and will be concerned most with getting cells in a short period of time, without regard to the efficiency of the sort; these sorts can be done at high speed where the efficiency is low but the speed of sorting is high. The bottom line is that speed and efficiency interact and both cannot be optimized at the same time. 9. Conclusions Flow cytometry has, arguably, remained a relatively constant technology since its entry in 1969 (10,11) into the modern era. The main technological changes that have occurred over the past 34 yr have been quantitative rather than qualitative. More parameters can now be analyzed simultaneously, more

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Fig. 15. Increasing reference to “flow cytometry” in the Medline-indexed literature over the past three decades. The actual use of flow cytometers predates the use of the term itself.

cells can be analyzed or sorted per second, and more sensitivity is available to detect fewer fluorescent molecules; in addition, flow cytometers are both smaller and less expensive than they were. However, a flow cytometer still involves particles flowing one by one past a laser beam, with photodetectors nestled around the analysis point to detect fluorescent or scattered light coming from the particles. By contrast with the less than radical changes in flow instrument technology, the increasing diversity of applications has been striking. For a start, the use of flow cytometry has increased remarkably; Fig. 15 indicates that references to “flow cytometry” in the Medline data base were zero in 1970, 113 in 1980, 2286 in 1990, and 4893 in the year 2000. But more important than the number of references is the range of applications that are now being addressed by flow cytometry. In the 1970s, leukocytes and cultured cells were the main particles analyzed by flow cytometry; now plankton, bacteria, disaggregated tissues, plant cells, viruses, chromosomes, latex beads, and DNA fragments are all, more or less, taken for granted. In addition, early flow cytometry looked at fluorescence emanating primarily from the stained proteins on the surface of cells or from stained DNA in their nuclei. Now plankton are examined for their autofluorescence, animal and plant cells are assayed for fluorescence that reflects their proliferative or metabolic function, sperm are sorted based on their X or

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Y genotype, many aspects of protein or DNA synthesis are assayed to indicate stage of cell cycle or of apoptosis, and bacteria are typed according to the size of their DNA fragments after restriction enzyme digestion. Indeed, flow cytometry has also been applied to beads, which are used to capture soluble analytes from the blood or culture medium; the beads, not the cells, are analyzed by flow cytometry to see how much of the analyte has been bound to their surface and, by comparison with standard curves, to indicate the concentration of analyte in the medium (34). Through its history, flow cytometry has sparked the collaboration of mathematicians, engineers, chemists, biologists, and physicians, working together to provide instrumentation that now probes not just our bodies and our culture flasks, but also the depths of the ocean (see ref. 58) and, potentially, life in space (or, at least, life in spaceships [59,60]). If nothing else, the example of flow cytometry should inspire us toward collaboration and to an open mind. Acknowledgments Howard Shapiro and Ben Verwer have provided me with advice on some of the electronic and illumination aspects of flow cytometry. I thank them for their help; all mistakes are very much my own. References 1. Moldavan, A. (1934) Photo-electric technique for the counting of microscopical cells. Science 80, 188–189. 2. Gucker Jr., F. T., O’Konski, C. T., Pickard, H. B., and Pitts Jr., J. N. (1947) A photoelectronic counter for colloidal particles. J. Am. Chem. Soc. 69, 2422–2431. 3. Cornwall, J. B. and Davison, R. M. (1950) Rapid counter for small particles in suspension. J. Sci. Instrum. 37, 414–417. 4. Coulter, W. H. (1956) High speed automatic blood cell counter and analyzer. Proc. Natl. Electronics Conf. 12, 1034–1040. 5. Bierne, T. and Hutcheon, J. M. (1957) A photoelectric particle counter for use in the sieve range. J. Sci. Instrum. 34, 196–200. 6. Kamentsky, L. A. and Melamed, M. R. (1965) Spectrophotometer: new instrument for ultrarapid cell analysis. Science 150, 630–631. 7. Kamentsky, L. A. and Melamed, M. R. (1967) Spectrophotometric cell sorter. Science 156, 1364–1365. 8. Fulwyler, M. J. (1965) Electronic separation of biological cells by volume. Science 150, 910–911. 9. Dittrich, W. and Göhde, W. (1969) Impulsfluorometrie dei einzelzellen in suspensionen. Z. Naturforsch. 24b, 360–361. 10. Van Dilla, M. A., Trujillo, T. T., Mullaney, P. F., and Coulter, J. R. (1969) Cell microfluorimetry: a method for rapid fluorescence measurement. Science 163, 1213–1214.

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11. Hulett, H. R., Bonner, W. A., Barrett, J., and Herzenberg, L. A. (1969) Cell sorting: automated separation of mammalian cells as a function of intracellular fluorescence. Science 166, 747–749. 12. Shapiro, H. M. (2003) Practical Flow Cytometry, 4th edit. Wiley-Liss, New York. 13. Melamed, M. R., Mullaney, P. F., and Shapiro, H. M. (1990) An historical review of the development of flow cytometers and sorters, in Flow Cytometry and Sorting, 2nd edit. (Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds.), Wiley-Liss, New York, pp. 1–8. 14. Melamed, M. R. (2001) A brief history of flow cytometry and sorting. Methods Cell Biol. 63(pt A), 3–17. 15. Van Dilla, M. A., Dean, P. N., Laerum, O. D., and Melamed, M. R., eds. (1985) Flow Cytometry: Instrumentation and Data Analysis. Academic Press, London. 16. Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds. (1990) Flow Cytometry and Sorting, 2nd edit. Wiley-Liss, New York. 17. Watson, J. V. (1991) Introduction to Flow Cytometry. Cambridge University Press, Cambridge. 18. Watson, J. V. (1992) Flow Cytometry Data Analysis: Basic Concepts and Statistics. Cambridge University Press, Cambridge. 19. Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds. (1997) Current Protocols in Cytometry. John Wiley & Sons, New York. 20. Diamond, R. A. and DeMaggio, S., eds. (2000) in Living Color: Protocols in Flow Cytometry and Cell Sorting. Springer-Verlag, Berlin. 21. Durack, G. and Robinson, J. P., eds. (2000) Emerging Tools for Single-Cell Analysis, Wiley-Liss, New York. 22. Ormerod, M. G., ed. (2000) Flow Cytometry: A Practical Approach, 3rd edit. Oxford University Press, Oxford. 23. Darzynkiewicz, Z., Crissman, H. A., and Robinson, J. P., eds. (2001) Cytometry: Methods in Cell Biology, 3rd edit., Vol. 63. Academic Press, San Diego. 24. Givan, A. L. (2001) Flow Cytometry: First Principles, 2nd edit. Wiley-Liss, New York. 25. Lloyd, D. (1993) Flow Cytometry in Microbiology. Springer-Verlag, London. 26. Alberghina, L., Porro, D., Shapiro, H., Srienc, F., and Steen, H., eds. (2000) Analysis of Microbial Cells at the Single Cell Level, J. Microbiol. Methods, Vol. 42. 27. Fugger, E. F., Black, S. H., Keyvanfar, K., and Schulman, J. D. (1998) Births of normal daughters after MicroSort sperm separation and intrauterine insemination, in-vitro fertilization, or intracytoplasmic sperm injection. Hum. Reprod. 13, 2367–2370. 28. Gledhill, B. L., Evenson, D. P., and Pinkel, D. (1990) Flow cytometry and sorting of sperm and male germ cells, in Flow Cytometry and Sorting, 2nd edit. (Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds.), Wiley-Liss, New York, pp. 531–551. 29. Reckerman, M. and Collin, F., eds. (2000) Aquatic Flow Cytometry: Achievements and Prospects, Scientia Marina, Vol. 64.

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30. Marie, D., Brussard, C. P. D., Thyrhaug, R., Bratbak, G., and Vaulot, D. (1999) Enumeration of marine viruses in culture and natural samples by flow cytometry. Appl. Environ. Microbiol. 59, 905–911. 31. Hedley, D. W. (1989) Flow cytometry using paraffin-embedded tissue: five years on. Cytometry 10, 229–241. 32. Gray, J. W. and Cram, L. S. (1990) Flow karyotyping and chromosome sorting, in Flow Cytometry and Sorting, 2nd edit. (Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds.), Wiley-Liss, New York. 33. Habbersett, R. C., Jett, J. H., and Keller, R. A. (2000) Single DNA fragment detection by flow cytometry, in Emerging Tools for Single-Cell Analysis (Durack, G. and Robinson, J. P., eds.), Wiley-Liss, New York, pp. 115–138. 34. Carson, R. T. and Vignali, D. A. A. (1999) Simultaneous quantitation of 15 cytokines using a multiplexed flow cytometric assay. J. Immunol. Methods 227, 41–52. 35. Steen, H. B. (2000) Flow cytometry of bacteria: glimpses from the past with a view to the future. J. Microbiol. Methods 42, 65–74. 36. Harkins, K. R. and Galbraith, D. W. (1987) Factors governing the flow cytometric analysis and sorting of large biological particles. Cytometry 8, 60–70. 37. Darzynkiewicz, Z., Juan, G., Li, X., Gorczyca, W., Murakami, T., and Traganos, F. (1997) Cytometry in cell necrobiology: Analysis of apoptosis and accidental cell death (necrosis). Cytometry 27, 1–20. 38. Gray, J. W., Dolbeare, F., and Pallavicini, M. G. (1990) Quantitative cell-cycle analysis, in Flow Cytometry and Sorting, 2nd edit. (Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds.), Wiley-Liss, New York, pp. 445–467. 39. Kim, Y., Jett, J. H., Larson, E. J., Penttila, J. R., Marrone, B. L., and Keller, R. A. (1999) Bacterial fingerprinting by flow cytometry: bacterial species discrimination. Cytometry 36, 324–332. 40. June, C. H., Abe, R., and Rabinovitch, P. S. (1997) Measurement of intracellular calcium ions by flow cytometry, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds.), John Wiley & Sons, New York, pp. 9.8.1–9.8.19. 41. Li, J. and Eastman, A. (1995) Apoptosis in an interleukin-2-dependent cytotoxic T lymphocyte cell line is associated with intracellular acidification. J. Biol. Chem. 270, 3203–3211. 42. Chow, S. and Hedley, D. (1997) Flow cytometric measurement of intracellular pH, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds.), John Wiley & Sons, New York, pp. 9.3.1–9.3.10. 43. Shapiro, H. M. (1997) Estimation of membrane potential by flow cytometry, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds.), John Wiley & Sons, New York, pp. 9.6.1–9.6.10. 44. Lyons, A. B. (1999) Divided we stand: tracking cell proliferation with carboxyfluorescein diacetate succinimidyl ester. Immunol. Cell Biol. 77, 509–515. 45. Crosland-Taylor, P. J. (1953) A device for counting small particles suspended in a fluid through a tube. Nature 171, 37–38.

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46. Kachel, V., Fellner-Feldegg, H., and Menke, E. (1990) Hydrodynamic properties of flow cytometry instruments, in Flow Cytometry and Sorting, 2nd edit. (Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds.), Wiley-Liss, New York, pp. 27–44. 47. Pinkel, D. and Stovel, R. (1985) Flow chambers and sample handling, in Flow Cytometry: Instrumentation and Data Analysis (Van Dilla, M. A., Dean, P. N., Laerum, O. D., and Melamed, M. R., eds.), Academic Press, London, pp. 77–128. 48. Salzman, G. C., Singham, S. B., Johnston, R. G., and Bohren, C. F. (1990) Light scattering and cytometry, in Flow Cytometry and Sorting, 2nd edit. (Melamed, M. R., Lindmo, T., and Mendelsohn, M. L., eds.), Wiley-Liss, New York, pp. 81–107. 49. Waggoner, A. (1997) Optical filter sets for multiparameter flow cytometry, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al. eds.), John Wiley & Sons, New York, pp. 1.5.1–1.5.8. 50. Verwer, B. (2002) BD FACSDiVa Option, BD Biosciences. 51. Bagwell, C. B., Baker, D., Whetstone, S., et al. (1989) A simple and rapid method of determining the linearity of a flow cytometer amplification system. Cytometry 10, 689–694. 52. Muirhead, K. A., Schmitt, T. C., and Muirhead, A. R. (1983) Determination of linear fluorescence intensities from flow cytometric data accumulated with logarithmic amplifiers. Cytometry 3, 251–256. 53. Wood, J. C. S. (1997) Establishing and maintaining system linearity, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds.), John Wiley & Sons, New York, pp. 1.4.1–1.4.12. 54. Seamer, L. (2000) Flow cytometry standard (FCS) data file format, in In Living Color: Protocols in Flow Cytometry and Cell Sorting (Diamond, R. A. and DeMaggio, S., eds.), Springer-Verlag, Berlin. 55. Loken, M. R. (1997) Multidimensional data analysis in immunophenotyping, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds.), John Wiley & Sons, New York, pp. 10.4.1–10.4.7. 56. Roederer, M., De Rosa, S., Gerstein, R., et al. (1997) 8 color, 10-parameter flow cytometry to elucidate complex leukocyte heterogeneity. Cytometry 29, 328–339. 57. Hoffman, R. A. and Houck, D. W. (1998) High speed sorting efficiency and recovery: Theory and experiment. Cytometry Suppl. 9, 142. 58. Dubelaar, G. B., Gerritzen, P. L., Beeker, A. E., Jonker, R. R., and Tangen, K. (1999) Design and first results of CytoBuoy: a wireless flow cytometer for in situ analysis of marine and fresh waters. Cytometry 37, 247–254. 59. Sams, C. F., Crucian, B. E., Clift, V. L., and Meinelt, E. M. (1999) Development of a whole blood staining device for use during space shuttle flights. Cytometry 37, 74–80. 60. Crucian, B. E. and Sams, C. F. (1999) The use of a spaceflight-compatible device to perform WBC surface marker staining and whole-blood mitogenic activation for cytokine detection by flow cytometry. J. Gravit. Physiol. 6, 33–34.

2 Multiparameter Flow Cytometry of Bacteria Howard M. Shapiro and Gerhard Nebe-von-Caron Summary The small size of bacteria makes some microbial constituents undetectable or measurable with only limited precision by flow cytometry. Bacteria may also behave differently from eukaryotes in terms of their interaction with dyes, drugs, and other reagents. It is therefore difficult to design multiparameter staining protocols that work, unmodified, across a wide range of bacterial species. This chapter describes reliable flow cytometric methods for assessment of the physiologic states of Gram-negative organisms, on the one hand, and Gram-positive organisms, on the other, based on measurement of membrane potential and membrane permeability. These techniques are useful in the assessment of effects of environmental conditions and antimicrobial agents on microorganisms.

Key Words Bacteria, cyanine dyes, flow cytometry, membrane permeability, membrane potential.

1. Introduction Although microscopy made us aware of the existence of the microbial world in the 17th century, it was not until the advent of cytometry in the late 20th century that it became possible to carry out detailed studies of microorganisms at the single-cell level. In principle, one can use a flow cytometer to measure the same parameters in bacteria or even viruses as are commonly measured in eukaryotic cells. However, the size, mass, nucleic acid, and protein content, and so forth of bacteria are approx 1/1000 the magnitude of the same parameters in mammalian cells, and this affects measurement quality. Low-intensity measurements typically exhibit large variances as a result of photoelectron statistics; some microbial constituents may thus be undetectable or measurable with only limited precision.

From: Methods in Molecular Biology: Flow Cytometry Protocols, 2nd ed. Edited by: T. S. Hawley and R. G. Hawley © Humana Press Inc., Totowa, NJ

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Bacteria also tend to behave differently from eukaryotes in terms of their interaction with reagents used in cytometry. Uptake and efflux of dyes, drugs, and other reagents by and from bacteria are affected by the structure of the cell wall, and by the presence of pores and pumps that may or may not be analogous to those found in eukaryotes. Moreover, the outer membrane of Gram-negative bacteria excludes most lipophilic or hydrophobic molecules, including reagents such as cyanine dyes. Although chemicals such as ethylenediaminetetraacetic acid (EDTA) may be used to permeabilize the outer membrane to lipophilic compounds with at least transient retention of some metabolic function, the characteristics of the permeabilized bacteria are distinct from those of organisms in the native state. Gram-positive organisms may take up a somewhat wider range of reagents without additional chemical treatment, but are no more predictable; for example, Walberg et al. (1) found substantial variability in patterns of uptake of different nucleic acid binding dyes by Gram-positive species. As one might guess from reading the preceding paragraph, it is, difficult, if not impossible, to design multiparameter staining protocols that will work, unmodified, across a wide range of bacterial genera and species. Both authors of this chapter have provided more general discussions of multiparameter flow cytometry of microorganisms elsewhere (2–4); here we concentrate on reliable methods developed in each of our laboratories for assessment of the physiologic states of Gram-negative organisms, on the one hand, and Gram-positive organisms, on the other. 1.1. Defining Bacterial “Viability”: Membrane Permeability vs Metabolic Activity Both microbiologists and cytometrists would like to be able to characterize microorganisms as viable or nonviable at the single-cell level; this is essential in determining effects of antimicrobial agents or adverse environmental conditions. A number of criteria for “viability” have been suggested; impermeability of the membrane to nucleic acid dyes such as propidium is one, and the presence of metabolic activity, as indicated by the production and retention of fluorescent product from a nonfluorescent enzyme substrate or by maintenance of a membrane potential, is another. However, until recently, relatively few investigators had reported making flow cytometric measurements of more than one of these characteristics in the same cells at the same time. Propidium (usually available as the iodide [PI]) and ethidium (usually available as the bromide [EB]) are structurally similar nucleic acid dyes; both contain a phenanthridinium ring, and both bind, with fluorescence enhancement, to double-stranded nucleic acids. However, ethidium has only a single positive charge; its N-alkyl group is an ethyl group. Ethidium and other dyes with a

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single delocalized positive charge are membrane permeant; that is, they cross intact prokaryotic and eukaryotic cytoplasmic membranes, although the dyes may be pumped out by efflux pumps. Propidium bears a double positive charge because its N-alkyl group is an isopropyl group with a quaternary ammonium substituent. Like a number of other dyes that also bear quaternary ammonium groups and more than one positive charge (e.g., TO-PRO-1, TO-PRO-3, and Sytox Green, all from Molecular Probes) propidium is generally believed to be membrane impermeant; that is, such dyes are excluded by prokaryotic and eukaryotic cells with intact cytoplasmic membranes. Cells that take up propidium and other multiply charged dyes are usually considered to be nonviable, although transient permeability to these dyes can be induced by certain chemical and physical treatments, for example, electroporation, with subsequent recovery of membrane integrity and viability. Thus, staining (or the lack thereof) with propidium is the basis of a so-called dye exclusion test of viability. Acid dyes, such as trypan blue and eosin, are also membrane impermeant and are used in dye exclusion tests. A variation on the dye exclusion test employs a nonfluorescent, membranepermeant substrate for an intracellular enzyme, which crosses intact or damaged cell membranes and which is then enzymatically cleaved to form a fluorescent, impermeant (or slowly permeant) product. The product is retained in cells with intact membranes, and quickly lost from putatively nonviable cells with damaged membranes. One commonly used substrate is diacetylfluorescein, also called fluorescein diacetate (FDA), which yields the slowly permeant fluorescein; nonfluorescent esters of some other fluorescein derivatives are better for dye exclusion tests because their products are less permeant (5). Another substrate is 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) (6); this is reduced by intracellular dehydrogenases to a fluorescent formazan, and provides an indication of respiratory activity as well as of membrane integrity. Bacteria normally maintain an electrical potential gradient (membrane potential, ΔΨ) of >100 mV across the cytoplasmic membrane, with the interior side negative. Charged dyes that are sufficiently lipophilic to pass readily through the lipid bilayer portion of the membrane partition across the membrane in response to the potential gradient. Positively charged lipophilic dyes, such as cyanines, are concentrated inside cells that maintain ΔΨ, while negatively charged lipophilic dyes, such as oxonols, are excluded. Thus, if two cells of the same volume, one with a transmembrane potential gradient and one without, were equilibrated with a cyanine dye, the cell with the gradient would contain more dye than the one without; if the cells were equilibrated with an oxonol dye, the cell without the gradient would contain more dye. However, cells with different volumes may contain different amounts of dye, irrespective of their ΔΨs, because it is the concentration of dye, rather than the amount of dye, in

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the cell that reflects ΔΨ. The flow cytometer measures the amount, not the concentration. When the cyanine dye 3,3′-diethyloxacarbocyanine iodide (DiOC2[3]) is added to cells at much higher concentrations than are normally used for flow cytometric estimation of ΔΨ, it is possible to detect red (~610 nm) fluorescence in addition to the green (~525 nm) fluorescence normally emitted by this dye (7); the red fluorescence is likely due to the formation of dye aggregates. At high dye concentrations, the green fluorescence is dependent on cell size, but independent of ΔΨ, whereas the red fluorescence is both size and potential dependent. The ratio of red and green fluorescence, which is largely independent of size, provides a more accurate and precise measurement of bacterial ΔΨ than can be obtained from simple fluorescence measurements. In theory, oxonol dyes should produce little or no staining of cells with normal ΔΨ and brighter staining of cells in which the potential gradient no longer exists. However, it is likely that the increased oxonol fluorescence seen in the heat-killed and alcohol-fixed bacteria often used as zero-potential controls reflects changes in size and in lipid and protein chemistry resulting from these treatments, as well as changes in ΔΨ. Decreases in ΔΨ of the Grampositive S. aureus produced by less drastic treatments, for example, nutrient deprivation, were detected by the ratiometric method using DiOC2(3) but produced no change in oxonol fluorescence (7). However, oxonol fluorescence does appear to increase with decreasing ΔΨ in Escherichia coli and other Gram-negative organisms (2). 1.2. Flow Cytometric Methods for Assessment of the Physiologic States of Gram-Negative and Gram-Positive Organisms The protocol described here for work with E. coli and other Gram-negative organisms (2,8,9) combines the oxonol dye bis-(1,3-dibutyl-barbituric acid) trimethine oxonol (DiBAC4[3]), which is used as an indicator of ΔΨ, with EB, which is retained by cells with intact membranes in which the efflux pump becomes inactive, as happens when energy metabolism is impaired. PI is used to demonstrate membrane permeability; once PI enters cells, it displaces EB from nucleic acids, presumably because PI has a higher binding affinity owing to its double positive charge. All three dyes are excited at 488 nm; DiBAC4(3) fluorescence is measured in a green (~525 nm) fluorescence channel, while EB and PI are, respectively, measured at ~575 nm and >630 nm. The protocol described here for work with S. aureus and other Gram-positive organisms uses the ratio of red (~610 nm) and green (~525 nm) fluorescence of DiOC2(3), excited at 488 nm, as an indicator of ΔΨ (7), and the far red (>695 nm) fluorescence of TO-PRO-3, excited by a red He–Ne (633 nm) or

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diode (635–640 nm) laser, to demonstrate membrane permeability. Dividing the TO-PRO-3 fluorescence signal by the green DiOC2(3) fluorescence signal produces a normalized indicator of permeability that provides better discrimination between cells with impermeable and permeable membranes than can be obtained from TO-PRO-3 fluorescence alone (10). 2. Materials Note: All aqueous solutions should be made with deionized distilled water (dH2O) and filtered through a filter with a pore size no larger than 0.22 μm. Dye solutions should be stored in the dark. 2.1. For DiBAC4(3)/EB/PI Staining 1. DiBAC4(3) (Molecular Probes, Eugene, OR) (FW 516.64): Oxonols may require addition of a base to be soluble. a. Stock solution: 10 mg/mL in dimethyl sulfoxide (DMSO), store at –20°C. b. Working solution: 10 or 100 μg/mL in dH2O, 0.5% Tween; store at 4°C. c. Final concentration: 10 μg/mL. 2. EB (Sigma-Aldrich, St. Louis, MO) (FW 394.3): a. Stock solution: 10 mg/mL in dH2O, store at –20°C. b. Working solution: 500 μg/mL in dH2O, store at 4°C. c. Final concentration: 10 μg/mL. 3. PI (Sigma-Aldrich) (FW 668.4): a. Stock solution: 2 mg/mL in dH2O; store at 4°C. b. Working solution: 500 μg/mL in dH2O; store at 4°C. c. Final concentration: 5 μg/mL. 4. Dulbecco’s buffered saline (DBS+), pH 7.2, with 0.1% peptone, 0.1% sodium succinate, 0.2% glucose, and 4 mM EDTA added.

2.2. For DiOC2(3)/TO-PRO-3 Staining 1. DiOC2(3) (Molecular Probes) (FW 460.31): a. Stock and working solution: 3 mM in DMSO; store at 4°C. b. Final concentration: 30 μM. 2. TO-PRO®-3 iodide (Molecular Probes) (FW 671.42): a. Stock and working solution: 1 mM in DMSO (supplied in this form); store at 4°C. b. Final concentration: 100 nM. 3. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) (Sigma-Aldrich) (FW 204.6): a. Stock and working solution: 2 mM in DMSO, store at 4°C. b. Final concentration: 15 μM. 4. Nisin (Sigma-Aldrich) (FW 3354): The preparation sold by Sigma-Aldrich contains 2.5% nisin, with the rest NaCl and dissolved milk solids; the filtered aqueous suspension must be diluted to achieve a final concentration of 25 μg/mL.

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5. Valinomycin (Sigma-Aldrich) (FW 1111): a. Stock and working solution: 2 mM in DMSO; store at 4°C. b. Final concentration: 5 μM. 6. Mueller–Hinton broth (Gibco™ Invitrogen Corporation, Carlsbad, CA) with 50 mg/L of Ca2+ (MHBc).

3. Methods 3.1. Functional Assessment of E. coli and Gram-Negatives Using DiBAC4(3)/EB/PI Staining (see Note 1) 3.1.1. Sample Preparation; Disaggregation of Bacteria by Ultrasound and Staining Procedure 1. For samples in liquid media, dilute 10 μL of sample in 200 μL of DBS+. Resuspend samples from solid media in DBS+ and then dilute further. 2. Optimize the fraction of single organisms in samples by gentle sonication in a Sanyo MSE Soniprep 150 apparatus (Sanyo, Chatsworth, CA) operating at 23 kHz. Place a 3-mm exponential probe, with its tip 5 mm below the liquid surface of a 2-mL sample, in a disposable polystyrene 7-mL flat-bottom container. Sonicate the sample for 2 min at 2 μm amplitude. 3. Add dyes: 10 μg/mL of DiBAC4(3), 10 μg/mL of EB, and 5 μg/mL of PI. 4. Keep the samples at 25°C for 30 min before running on the flow cytometer.

3.1.2. Flow Cytometry 1. Use 488 nm as the excitation wavelength. 2. Use forward and/or side scatter signals for triggering. A software gate excluding low-level scatter signals may be set to remove events due to noise and particulate contaminants in samples. 3. Set up detector filters so that PI fluorescence is measured above 630 nm, EB fluorescence at 575 nm, and DiBAC4(3) fluorescence at 525 nm. 4. Adjust hardware or software compensation to minimize fluorescence of each dye in channels used primarily for measurement of other dyes. 5. For viability determination, single cells may be sorted directly onto nutrient agar plates.

3.1.3. Results

Figure 1 shows the results of a sorting experiment in which Salmonella typhimurium stored for 25 d on nutrient agar at 4°C was resuspended in DBS, sonicated to break up aggregates, and stained with DiBAC4(3), EB, and PI. The dye combination delineates cells in different functional stages. Active pumping cells do not stain significantly with any of the dyes. Deenergized cells take up ethidium, but not DiBAC4(3) or propidium. Depolarized cells take up ethidium and DiBAC4(3), but not propidium, and permeabilized cells and “ghosts,” that is, cells with damaged membranes, take up both DiBAC4(3) and

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Fig. 1. DiBAC4(3)/EB/PI staining delineates different functional stages of Salmonella typhimurium (stored for 25 d on nutrient agar at 4°C). Cells corresponding to the different functional stages were sorted onto nutrient agar plates to monitor recovery.

propidium. In most cases, all but the permeabilized cells are capable of recovery. In the experiment shown in the figure, approx one third of the electrically depolarized cells grew on agar plates; depolarization therefore indicates a decline in cell functionality, but certainly not cell death. Recovery of actively pumping and deenergized cells typically approaches 100%; deenergized cells lose pump activity but maintain ΔΨ at least briefly. Fewer than 1% of events sorted from the regions containing permeabilized cells and ghosts will form colonies on agar. 3.2. Measurement of ΔΨ and Permeability Using DiOC2(3) and TO-PRO-3 (see Note 2) 3.2.1. Sample Preparation 1. Dilute samples in MHBc to a target concentration of 106–107 cells/mL. 2. Add dyes: 30 μM DiOC2(3) and 100 nM TO-PRO-3. 3. Keep the samples at room temperature (~25°C) for 5 min before running on the flow cytometer.

3.2.2. Flow Cytometry and Data Analysis 1. Use an instrument with 488 nm (argon-ion or solid-state laser) and red (633 nm from a He–Ne laser or approx 635 nm from a diode laser) excitation beams. 2. Use forward or side scatter as the trigger signal. A software gate may be set to exclude low-level scatter signals produced by noise and debris.

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3. DiOC2(3) is excited at 488 nm; its green fluorescence is detected through a 525to 530-nm bandpass filter with approx 20 nm bandwidth and its red fluorescence is detected through a 610-nm bandpass filter with approx 20 nm bandwidth. 4. TO-PRO-3™ is excited by the red laser, and its far red fluorescence is detected through one or two 695-nm longpass color glass filters.

In instruments in which data are collected using logarithmic amplifiers, a quantity proportional to the ratio of [DiOC2(3) red fluorescence]/[DiOC2(3) green fluorescence] is calculated by adding a constant to the red fluorescence channel value and subtracting the green fluorescence channel value (7). The addition of a constant value is necessary to keep values of the calculated parameter on the same scale as is used for the raw fluorescence measurements. For a 256-channel logarithmic scale, with 64 channels per decade, a constant value of 96 is convenient; the calculated parameter, which serves as a measure of ΔΨ, then represents the log of (103/2 × [red fluorescence/green fluorescence]). A normalized permeability value, based on the ratio of [TO-PRO-3 fluorescence]/[DiOC2(3) green fluorescence], is derived in the same manner. If highresolution linear data are available, ratios may be calculated directly by division and multiplied by appropriate scaling constants. Different mechanisms for perturbing ΔΨ and permeability are incorporated into control samples. After 5–15 min of incubation, CCCP (15 μM) reduces ΔΨ to zero, but does not affect permeability; nisin (25 μg/mL) reduces ΔΨ to zero, and also renders organisms permeable to TO-PRO-3. Measurements of ΔΨ using DiOC2(3) may be calibrated by controlled application of valinomycin in the presence of different external potassium ion concentrations (7). The red/green fluorescence ratio is measured for cells in a range of buffers containing 5 μM valinomycin and various concentrations of potassium; the concentration of sodium ion is adjusted to keep the combined molarity of potassium and sodium at 300 mM. Figure 2 plots the membrane potential of amoxicillin-treated S. aureus against normalized permeability. The strain of S. aureus used was amoxicillin sensitive; aliquots were exposed to concentrations of amoxicillin above (1 μg/mL) and below (0.5 μg/mL) the minimal inhibitory concentration (MIC). In cultures treated with either dose, at time zero, most cells show low values of permeability and relatively high values of ΔΨ, appearing in the lower right quadrant of the display. After 2 h at an amoxicillin concentration above MIC (top strip), many cells have lost ΔΨ completely, and most have lost ΔΨ to some extent (lower and upper left quadrants); over 58% of the total have become permeable (upper left quadrant). By 4 h, some regrowth has occurred; about 17% of the events measured show normal ΔΨ and no permeability. The situation is quite different at a sub-MIC amoxicillin concentration (bottom strip). At 2, 3, and even 4 h, a substantial fraction of events (as high as 28%) are in the

41

Fig. 2. DiOC2(3)/TO-PRO-3 staining reveals the response of S. aureus exposed to different concentrations of amoxicillin for different lengths of time. Membrane potential (the ratio of DiOC2(3) red to DiOC2(3) green fluorescence, log scale, x-axis) is plotted against normalized permeability (the ratio of TO-PRO-3 far red to DiOC2 (3) green fluorescence, log scale, y-axis).

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upper right quadrant, indicating a ΔΨ greater than zero with permeability to TO-PRO-3. By 4 h, most cells (>79%) have regained normal ΔΨ and lost permeability. Bacterial counts over this time period rule out the accumulation of a high-ΔΨ, impermeable population by expansion of the small population of such cells present after 2 h. Although some intermediate-ΔΨ, permeable events may represent aggregates of high-ΔΨ, impermeable viable cells and permeable, lowΔΨ dead cells, many of these events appear to be accounted for by TO-PRO-3 uptake into viable cells. This, parenthetically, suggests a novel approach to antimicrobial therapy (3,4,11). 4. Notes 1. DiBAC4(3)/EB/PI staining: This methodology has been shown to work in some Gram-positive species, for example, Micrococcus lysodeikticus, and in yeasts (9). Some adjustment of DiBAC4(3) concentration may be needed depending on the concentration of organisms and lipophilic components in samples; concentrations as low as 0.1 μg/mL have been used with samples containing small numbers of cells. 2. DiOC2(3)/TO-PRO-3 staining: This method has been used in instruments with 488 nm and red illuminating beams separated in space; it is not known whether it will work in instruments with collinear 488 nm and red beams. Both DiOC2(3) and TO-PRO-3 adhere to the tubing used in most flow cytometers, and the high concentration of cyanine dye used in this protocol may necessitate replacement of some tubing if repeated cleaning with dilute chlorine bleach, ethanol, detergents, and so forth still leaves dye in the system. Some bacterial types (e.g., S. aureus) may be grown in culture following exposure to 30 μM DiOC2(3). The method has been used with some Gram-negative species, for example, E. coli, with 5 mM EDTA added to staining solutions, and delineates cells with various apparent values of ΔΨ as well as discriminating those that do and do not take up TO-PRO-3. However, Gram-negative bacteria appear to be damaged by the calibration buffers used with Gram-positive organisms, and it has not been possible to derive calibration curves for the former.

Acknowledgments The authors thank Chris Hewitt, Dave Novo, Nancy Perlmutter, and Jared Silverman, who have played vital roles in the development and application of the methods described here. References 1. Walberg, M., Gaustad, P., and Steen, H. B. (1999) Uptake kinetics of nucleic acid targeting dyes in S. aureus, E. faecalis and B. cereus: a flow cytometric study. J. Microbiol. Methods 35, 167–176. 2. Nebe-von-Caron, G., Stephens, P. J., Hewitt, C. J., Powell, J. R., and Badley, R. A. (2000) Analysis of bacterial function by multi-colour fluorescence flow cytometry and single cell sorting. J. Microbiol. Methods 42, 97–114.

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3. Shapiro, H. M. (2000) Microbial analysis at the single-cell level: tasks and techniques. J. Microbiol. Methods 42, 3–16. 4. Shapiro, H. M. (2003). Practical Flow Cytometry, 4th edit. Wiley-Liss, Hoboken, NJ. 5. Haugland, R. P. (2002) Handbook of Fluorescent Probes and Research Products, 9th edit., Molecular Probes, Eugene, OR. (online at www.probes.com) 6. Davey, H. M. and Kell, D. B. (1996) Flow cytometry and cell sorting of heterogeneous microbial populations-the importance of single-cell analyses. Microbiol. Revs. 60, 641–696. 7. Novo, D., Perlmutter, N. G., Hunt, R. H., and Shapiro, H. M. (1999) Accurate flow cytometric membrane potential measurement in bacteria using diethyloxacarbocyanine and a ratiometric technique. Cytometry 35, 55–63. 8. Hewitt, C. J., Nebe-von Caron, G., Nienow, A. W., and McFarlane, C. M. (1999) Use of multi-staining flow cytometry to characterise the physiological state of Escherichia coli W3110 in high cell density fed-batch cultures. Biotechnol. Bioeng. 63, 705–711. 9. Hewitt, C. J. and Nebe-Von-Caron, G. (2004) The application of multi-parameter flow cytometry to monitor individual microbial cell physiological state, in Physiological Stress Responses in Bioprocesses: Advances in Biochemical Engineering/ Biotechnology (Enfors, S.-V., ed.), Springer-Verlag, Heidelberg, Germany. 10. Novo, D. J., Perlmutter, N. G., Hunt, R. H., and Shapiro, H. M. (2000) Multiparameter flow cytometric analysis of antibiotic effects on membrane potential, membrane permeability, and bacterial counts of Staphylococcus aureus and Micrococcus luteus. Antimicrob. Agents Chemother. 44, 827–834. 11. Shapiro, H. M. (2001) Multiparameter flow cytometry of bacteria: implications for diagnostics and therapeutics. Cytometry 43, 223–226.

3 Multiparameter Data Acquisition and Analysis of Leukocytes Carleton C. Stewart and Sigrid J. Stewart Summary For data acquisition, each supplier provides the software necessary and unique to its instrument. For data analysis, the same software may be used. In addition, several second party vendors provide software often with more capabilities than that provided by the instrument companies. Because of the increase in multiparameter data acquisition, we describe one method for validating instrument performance prior to data acquisition. The fundamentals of data analysis leading to a generic strategy for analysis of any number of parameters are described. This generic approach is designed to simplify the increasing complexity of multiparameter data analysis.

Key Words Bivariate histograms, color gating, gating, instrument performance, phenogram, univariate.

1. Introduction Several software packages are currently available for the analysis of flow cytometry data. While each of them is unique in the way they process the data, the general strategies are similar. Because the complexity of analysis increases with the number of measured parameters, we focus on both the classical approaches as well as introduce a generic approach that can be utilized for any number of parameters. A parameter describes what is measured. A channel describes the value of the measurement. There are three kinds of parameters: forward scatter (FSC), side scatter (SSC), and fluorescence. FSC is measured between 2° and 22° from the laser beam (depending on instrument manufacturer), and it is proportional to the cross-sectional area of the particle. Because there are other factors that affect the measurement, it is only an estimate of size. SSC is also called orthogonal or 90° scatter because it is measured at 90° From: Methods in Molecular Biology: Flow Cytometry Protocols, 2nd ed. Edited by: T. S. Hawley and R. G. Hawley © Humana Press Inc., Totowa, NJ

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to the laser beam, and it is sensitive to cell granularity provided the granules’ index of refraction is different from that of the cytosol. The intensity of fluorescence is also measured orthogonal to the cell stream and it provides quantitative measurements from any number of resolvable colored fluorochromes used in the cell staining process. We do not cover sample preparation in this chapter (1,2). The most commonly used fluorochromes that are conjugated to the primary antibody, secondary antibodies, or avidin can be excited at 488 nm or approx 633 nm. Those excited at 488 nm are fluorescein isothiocyanate (FITC), phycoerythrin (PE), a phycoerythrin–Texas red tandem complex (PE–TR), a phycoerythrin–cyanine 5 tandem complex (PE–CY5), peridinin chlorophyll protein (PerCP), a phycoerythrin–cyanine 7 tandem complex (PE–CY7), and several Alexa dyes from Molecular Probes (Eugene, OR). Their fluorescence emission wavelengths are: FITC = 530 nm, PE = 575 nm, PE–TR = 613 nm, PE–CY5 or PerCP = 670 nm, and PE–CY7 >700 nm. Other fluorochromes can be excited at 633 nm with a He–Ne laser or 635 nm with a red diode laser. Their fluorescence emission wavelengths are: CY5, APC, or Alexa 648 = 675 nm, and APC–CY7 >700 nm. Note that the tandem dyes consist of a donor fluorochrome, often phycoerythrin, and an acceptor molecule such as TR, CY5, or CY7, covalently linked to create a fluorochrome with a greater difference between its excitation and emission. Antibodies can be conjugated with different fluorochromes of different excitation and/or emission properties (colors) so they can each be resolved. To accomplish color separation, spectral filters and dichroic mirrors are used that reflect or transmit specific wavelengths. Because the fluorochrome’s emission wavelengths can be very broad, it is also necessary to remove unwanted overlapping fluorescence by appropriately adjusting the instrument’s compensation circuits or by using software compensation. To perform this task it is necessary to use compensation standards. For more information on compensation additional reading is recommended (3–5). All flow cytometers collect data in the same way using a process called LIST MODE. A standard list mode file includes a header containing information about the sample and instrument followed by a list of data in the order collected (6). The values that are stored in a list mode file are the voltages from the detectors for each parameter (P1, P2, P3, . . . Pn) after they have been electronically processed. As shown in Table 1, the data in a list mode file consists of the channel number corresponding to the value for each parameter for cell 1, followed by cell 2, and so forth until the last cell, n, is measured. If six parameters are measured for 10,000 cells, the file will contain 60,000 numbers in the order they are acquired.

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Table 1 Correlated List Mode File: Values for Each Parameter Cell

P1

P2

P3

Pn

C1 C2 C3 C4 Cn

122 424 186 101 330

84 92 83 98 79

120 120 562 487 130

440 460 122 133 452

2. Materials 1. 2. 3. 4. 5.

A flow cytometer cell sorter and associated computer/software. Beads for alignment. A source of leukocytes. Fluorescently conjugated antibodies to desired cell populations. Solutions and reagents needed for cell staining.

3. Methods The methods described below include instrument performance validation, data displays, and gating strategies. 3.1. Evaluating Instrument Performance 1. Before acquiring data, it is most important to assess instrument performance. To accomplish this, a process is established that can be easily applied for comparing the present day’s performance with that of the previous day. Usually good quality microspheres are evaluated, and their median fluorescence intensity and coefficient of variation measured. 2. A threshold is established for each functioning parameter, and when the values are outside the threshold, corrective action must be taken. Figure 1 illustrates the performance of a FACSCalibur operating every day for 1 yr. To ensure stability of performance, a preventative maintenance program should be established and maintained. 3. Because flow cytometers are used to measure cells, the final verification of performance needs to be cell based. A cell system is chosen that is relevant to the activity for which the instrument will be used. 4. As illustrated in Fig. 2 for immunophenotyping, cells are stained with an antibody of each fluorochrome and their fluorescence intensity measured. Regions for the target population are drawn to produce a template that is used daily. All cells must appear in their respective regions for the instrument to pass the verification.

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Fig. 1. Daily performance of a FACSCalibur. A Levi–Jennings plot of the peak fluorescence intensity of FL1 measured daily for 1 yr is shown. The FACSCalibur appears to be more stable than the microspheres used as the peak changes to new values when differing lots of microspheres are used. The coefficient of variation (not shown) must be 12 h). Incubating with antigen prior to addition of brefeldin A is recommended only for whole protein antigens (which require processing by antigen-presenting cells). An incubation period of 2 h in antigen alone is optimal for CD4 responses to protein antigens (15). CD8 responses to whole protein antigens can sometimes be induced with longer incubation in antigen alone, but not in all donors (19). 8. Automated activation/stopping point: Activation can be terminated by cooling cells to 18°C prior to processing (end of Subheading 3.2.). This process can be automated using a programmable heat block or water bath. 9. Batching of samples: Samples can be frozen at –80°C at the end of step 4, Subheading 3.3.1. (or 3.3.2. for PBMC). Because they are fixed, they need not be moved into a special freezing medium, but can be frozen directly in cell fixation buffer (15,36). In this fashion, samples can be accumulated for shipping to another

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10.

11.

12.

13.

14.

15.

16.

Maecker laboratory, or for later batch analysis. Stability of frozen activated samples has been tested for up to 6 mo without loss of signal (unpublished data). Temperature of lysing and permeabilizing solutions: Fixation and permeabilization of cells are temperature dependent. Solutions for these steps should be stored and used at controlled room temperature. If ambient temperatures vary significantly above or below 22–25°C, a temperature-controlled incubation should be done. Centrifugation speed: Fixation and permeabilization cause increased cell buoyancy. All centrifugation steps after fixation should therefore be carried out at 500g to avoid excessive cell loss. Importance of washing: Because of the small wash volumes in 96-well plates, effective washing (without significant cell loss) is essential. Sufficient washing prior to addition of staining antibodies is at least as important as washing after intracellular staining. Use of appropriate-length vacuum manifolds is critical to achieving consistent washing without undue cell loss. Vacuum manifolds should be frequently cleaned with bleach to prevent clogging. Surface vs intracellular staining of surface antigens: The protocols outlined here use a single intracellular staining step for all antibodies, which is possible using the antibodies provided in commercial kits (FastImmune, BD Biosciences). Staining CD3, CD4, and/or CD8 intracellularly reduces the signal-to-noise ratio relative to surface staining (prior to fixation), but decreases the down-modulation of these antigens seen with activation. Automation of acquisition and analysis: In addition to the higher throughput realized by processing samples in 96-well plates, automated acquisition with a plate loader and automated batch analysis using gating algorithms (Fig. 1) can greatly reduce sample analysis time. Furthermore, the results compare favorably to results obtained in tubes and using manual gating schemes (35). Number of events to collect: Detection of small populations of antigen-specific cells requires collection of a large number of relevant events. This protocol suggests collecting 40,000 CD4 or CD8 T cells, which is sufficient to distinguish a 0.1% response from a background of 0.02% with reasonable statistical significance. A standard power calculation for determining sample size can be used to assess whether the difference between two proportions is statistically significant, based on the number of events collected (37). Importance of gating: Improper gating is a frequent source of quantitative variation in results. It is particularly important to include cells with lower levels of CD3, CD4, and/or CD8, as these antigens are down-modulated on activation. Also, “response regions” should be set with reference to positive control samples, to include all relevant cells, as well as with reference to negative control samples, to exclude nonspecifically stained cells.

Acknowledgments The author thanks Maria Suni and Holli Dunn for providing data and protocol development and Laurel Nomura and Vernon Maino for critical review of the manuscript.

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References 1. Jung, T., Schauer, U., Heusser, C., Neumann, C., and Rieger, C. (1993) Detection of intracellular cytokines by flow cytometry. J. Immunol. Methods 159, 197–207. 2. Prussin, C. and Metcalfe, D. D. (1995) Detection of intracytoplasmic cytokine using flow cytometry and directly conjugated anti-cytokine antibodies. J. Immunol. Methods 188, 117–128. 3. Picker, L. J., Singh, M. K., Zdraveski, Z., et al. (1995) Direct demonstration of cytokine synthesis heterogeneity among human memory/effector T cells by flow cytometry. Blood 86, 1408–1419. 4. Nylander, S. and Kalies, I. (1999) Brefeldin A, but not monensin, completely blocks CD69 expression on mouse lymphocytes: efficacy of inhibitors of protein secretion in protocols for intracellular cytokine staining by flow cytometry. J. Immunol. Methods 224, 69–76. 5. Waldrop, S. L., Pitcher, C. J., Peterson, D. M., Maino, V. C., and Picker, L. J. (1997) Determination of antigen-specific memory/effector CD4+ T cell frequencies by flow cytometry: evidence for a novel, antigen-specific homeostatic mechanism in HIV-associated immunodeficiency. J. Clin. Invest. 99, 1739–1750. 6. Suni, M. A., Picker, L. J., and Maino, V. C. (1998) Detection of antigen-specific T cell cytokine expression in whole blood by flow cytometry. J. Immunol. Methods 212, 89–98. 7. Maecker, H. T., Maino, V. C., and Picker, L. J. (2000) Immunofluorescence analysis of T-cell responses in health and disease. J. Clin. Immunol. 20, 391–399. 8. Ghanekar, S. A. and Maecker, H. T. (2003) Cytokine flow cytometry: multiparametric approach to immune function analysis. Cytotherapy 5, 1–6. 9. Scheffold, A., Assenmacher, M., Reiners-Schramm, L., Lauster, R., and Radbruch, A. (2000) High-sensitivity immunofluorescence for detection of the pro- and antiinflammatory cytokines gamma interferon and interleukin-10 on the surface of cytokine-secreting cells. Nat. Med. 6, 107–110. 10. Brosterhus, H., Brings, S., Leyendeckers, H., et al. (1999) Enrichment and detection of live antigen-specific CD4(+) and CD8(+) T cells based on cytokine secretion. Eur. J. Immunol. 29, 4053–4059. 11. Maecker, H. T., Dunn, H. S., Suni, M. A., et al. (2001) Use of overlapping peptide mixtures as antigens for cytokine flow cytometry. J. Immunol. Methods 255, 27–40. 12. Waldrop, S. L., Davis, K. A., Maino, V. C., and Picker, L. J. (1998) Normal human CD4+ memory T cells display broad heterogeneity in their activation threshold for cytokine synthesis. J. Immunol. 161, 5284–5295. 13. Pitcher, C. J., Quittner, C., Peterson, D. M., et al. (1999) HIV-1-specific CD4+ T cells are detectable in most individuals with active HIV-1 infection, but decline with prolonged viral suppression. Nat. Med. 5, 518–525. 14. Suni, M. A., Ghanekar, S. A., Houck, D. W., et al. (2001) CD4(+)CD8(dim) T lymphocytes exhibit enhanced cytokine expression, proliferation and cytotoxic activity in response to HCMV and HIV-1 antigens. Eur. J. Immunol. 31, 2512–2520.

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15. Nomura, L. E., Walker, J. M., and Maecker, H. T. (2000) Optimization of whole blood antigen-specific cytokine assays for CD4(+) T cells. Cytometry 40, 60–68. 16. Ghanekar, S. A., Nomura, L. E., Suni, M. A., Picker, L. J., Maecker, H. T., and Maino, V. C. (2001) Gamma interferon expression in CD8(+) T cells is a marker for circulating cytotoxic T lymphocytes that recognize an HLA A2-restricted epitope of human cytomegalovirus phosphoprotein pp65. Clin. Diagn. Lab Immunol. 8, 628–631. 17. Maino, V. C., Suni, M. A., Wormsley, S. B., Carlo, D. J., Wallace, M. R., and Moss, R. B. (2000) Enhancement of HIV type 1 antigen-specific CD4+ T cell memory in subjects with chronic HIV type 1 infection receiving an HIV type 1 immunogen. AIDS Res. Hum. Retroviruses 16, 539–547. 18. Maecker, H. T., Auffermann-Gretzinger, S., Nomura, L. E., Liso, A., Czerwinski, D. K., and Levy, R. (2001) Detection of CD4 T-cell responses to a tumor vaccine by cytokine flow cytometry. Clin. Cancer Res. 7, 902s–908s. 19. Maecker, H. T., Ghanekar, S. A., Suni, M. A., He, X. S., Picker, L. J., and Maino, V. C. (2001) Factors affecting the efficiency of CD8+ T cell cross-priming with exogenous antigens. J. Immunol. 166, 7268–7275. 20. Asanuma, H., Sharp, M., Maecker, H. T., Maino, V. C., and Arvin, A. M. (2000) Frequencies of memory T cells specific for varicella-zoster virus, herpes simplex virus, and cytomegalovirus by intracellular detection of cytokine expression. J. Infect. Dis. 181, 859–866. 21. Bitmansour, A. D., Douek, D. C., Maino, V. C., and Picker, L. J. (2002) Direct ex vivo analysis of human CD4(+) memory T cell activation requirements at the single clonotype level. J. Immunol. 169, 1207–1218. 22. Bitmansour, A. D., Waldrop, S. L., Pitcher, C. J., et al. (2001) Clonotypic structure of the human CD4(+) memory T cell response to cytomegalovirus. J. Immunol. 167, 1151–1163. 23. Dunn, H. S., Haney, D. J., Ghanekar, S. A., Stepick-Biek, P., Lewis, D. B., and Maecker, H. T. (2002) Dynamics of CD4 and CD8 T cell responses to cytomegalovirus in healthy human donors. J. Infect. Dis. 186, 15–22. 24. He, X. S., Rehermann, B., Lopez-Labrador, F. X., et al. (1999) Quantitative analysis of hepatitis C virus-specific CD8(+) T cells in peripheral blood and liver using peptide-MHC tetramers. Proc. Natl. Acad. Sci. USA 96, 5692–5697. 25. Jacobson, M. A., Schrier, R., McCune, J. M., et al. (2001) Cytomegalovirus (CMV)-specific CD4+ T lymphocyte immune function in long-term survivors of AIDS-related CMV end-organ disease who are receiving potent antiretroviral therapy. J. Infect. Dis. 183, 1399–1404. 26. Karanikas, V., Lodding, J., Maino, V. C., and McKenzie, I. F. (2000) Flow cytometric measurement of intracellular cytokines detects immune responses in MUC1 immunotherapy. Clin. Cancer Res. 6, 829–837. 27. Kern, F., Faulhaber, N., Frommel, C., et al. (2000) Analysis of CD8 T cell reactivity to cytomegalovirus using protein-spanning pools of overlapping pentadecapeptides. Eur. J. Immunol. 30, 1676–1682.

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28. Kern, F., Surel, I. P., Brock, C., et al. (1998) T-cell epitope mapping by flow cytometry. Nat. Med. 4, 975–978. 29. Kern, F., Surel, I. P., Faulhaber, N., et al. (1999) Target structures of the CD8(+)-T-cell response to human cytomegalovirus: the 72-kilodalton major immediate-early protein revisited. J. Virol. 73, 8179–8184. 30. Komanduri, K. V., Donahoe, S. M., Moretto, W. J., et al. (2001) Direct measurement of CD4+ and CD8+ T-cell responses to CMV in HIV-1- infected subjects. Virology 279, 459–470. 31. Komanduri, K. V., Feinberg, J., Hutchins, R. K., et al. (2001) Loss of cytomegalovirus-specific CD4+ T cell responses in human immunodeficiency virus type 1-infected patients with high CD4+ T cell counts and recurrent retinitis. J. Infect. Dis. 183, 1285–1289. 32. Komanduri, K. V., Viswanathan, M. N., Wieder, E. D., et al. (1998) Restoration of cytomegalovirus-specific CD4+ T-lymphocyte responses after ganciclovir and highly active antiretroviral therapy in individuals infected with HIV-1. Nat. Med. 4, 953–956. 33. Mosca, P. J., Hobeika, A. C., Clay, T. M., Morse, M. A., and Lyerly, H. K. (2001) Direct detection of cellular immune responses to cancer vaccines. Surgery 129, 248–254. 34. Maecker, H. T. and Maino, V. C. (2002) Flow cytometric analysis of cytokines, in Manual of Clinical Laboratory Immunology, 6th edit. (Hooks, J., ed.), ASM Press, Washington, DC. 35. Suni, M. A., Dunn, H. S., Orr, P. L., et al. (2003) Optimization of plate-based cytokine flow cytometry assays. BMC Immunol. 4, 9. 36. Nomura, L. E., deHaro, E. D., Martin, L. N., and Maecker, H. T. (2003) Optimal preparation of rhesus macaque blood for cytokine flow cytometry analysis. Cytometry in press. 37. Motulsky, H. (1995) Intuitive Biostatistics. Oxford University Press, Oxford.

6 Use of Cell-Tracking Dyes to Determine Proliferation Precursor Frequencies of Antigen-Specific T Cells Alice L. Givan, Jan L. Fisher, Mary G. Waugh, Nadège Bercovici, and Paul K. Wallace Summary The T-cell receptor provides T cells with specificity for antigens of particular molecular structure (the “epitope”); the T-cell pool in an individual responds to the presence of many different antigenic epitopes, but any particular T cell will respond preferentially to one defined epitope. After stimulation of a T cell by the binding of its receptor to its cognate antigen in the context of a major histocompatibility complex (MHC) molecule on an antigen-presenting cell, the T cell will begin to proliferate and synthesize cytokines. Tetramer binding and the enzyme-linked immunospot (ELISPOT) method have been used to determine what proportion of cells in the T-cell pool can bind to a defined antigenic peptide or will secrete cytokines in response to a particular antigenic stimulation. The method described here uses tracking dyes to determine what proportion of T cells will proliferate in response to stimulation. As a flow cytometric “single-cell” method, it can be combined with tetramer and cytokine staining to determine the precursor frequencies of cells in the T-cell pool able to bind tetramer, to synthesize cytokines, and to proliferate in response to antigen.

Key Words Antigen specificity, carboxyfluorescein diacetate succinimidyl ester, cytokine synthesis, PKH, precursor frequency, proliferation, T cell, tetramers, tracking dye.

1. Introduction Receptors on T cells bind to peptides presented in the context of major histocompatibility complex (MHC) class I or class II molecules on antigen-presenting cells. The T-cell receptor, by its structure, conveys antigen specificity to a T cell: any particular T cell will interact with and respond to presented peptide with a From: Methods in Molecular Biology: Flow Cytometry Protocols, 2nd ed. Edited by: T. S. Hawley and R. G. Hawley © Humana Press Inc., Totowa, NJ

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defined epitope (that is, a 9- to 14-amino-acid peptide fragment that is an antigenic determinant). The entire T-cell pool in an individual contains cells that are specific to a wide variety of antigenic epitopes, but any particular T cell will respond preferentially to a particular or very closely related epitope. In the naïve state, T cells of particular specificity exist as a low percentage of the T-cell pool. After binding to presented antigen of the cognate specificity, T cells respond in various ways toward the goal of acquiring effector and memory functions, including cytokine synthesis and cytolytic activity as well as proliferation and longterm survival. During the period immediately after stimulation, T cells of particular specificity will exist in high numbers, that is, as a high proportion of the T-cell pool. At some period of time after stimulation, these T cells will decrease in number but will remain in higher numbers than before stimulation (that is, while in the naïve state). Because the proportion of T cells with any particular specificity changes in response to the history of past stimulation, determining this proportion is informative with regard to assessing past contact with antigens and also with regard to assessing the readiness of T cells to react to future stimulation (e.g., to reinfection or to transplantation or to malignancy). While determining the number of T cells with particular antigen specificity is important, methods for making this determination are problematic. The difficulty results, in part, from the low frequency of T cells specific for a defined epitope; a relevant methodology needs to be able to detect rare cells. In addition, there is no “gold standard” for the definition of an antigen-specific cell. The “classical” responses of a T cell to antigen involve, first, binding to the antigen via the antigen receptor, then secretion of cytokines and proliferation, and finally the acquisition of effector function. Therefore, valid methods used, in the past, for determination of the number of T cells with a particular antigen receptor have involved assaying the ability of T cells to bind to peptides (by using fluorochrome-conjugated tetramers [1]); assaying the proportion of cells that synthesize cytokine in response to antigen (with flow cytometry [2] or with the enzyme-linked immunospot [ELISPOT] method [3]); and assaying the number of cells proliferating in response to antigen (traditionally by looking at tritiated thymidine incorporation by the limiting dilution assay [LDA] [4] ). During proliferation of a few cells with rare specificity, that small number of cells will expand and continually increase its representation in the pool of mainly nondividing cells (Fig. 1). It is, therefore, important to calculate the precursor frequency of proliferating cells in order to know the antigen-specific proliferative potential of the cells in the initial resting population (before stimulation). The flow cytometric method described here (5–8) uses cell tracking dyes as a simple replacement for the LDA method to determine the proportion of cells that will proliferate in response to antigen (see Note 1). Cells are stained with a tracking dye before culture. During cell division, the tracking dye is par-

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Fig. 1. Expansion of flu-peptide-tetramer-positive/CD8-positive T cells after 6 d of culture with flu peptide stimulation. The percentages indicate the tetramer-positive/ CD8+ cells among live lymphocytes.

titioned between daughter cells, so that each division brings about a halving of fluorescence intensity; the intensity of a cell, by comparison with the intensity of resting cells, provides an indication of how many divisions the cell has undergone since stimulation (Fig. 2). Analysis of the staining levels of cells in the flow cytometric data file acquired after several days of culture provides the ability to calculate back to the precursor frequency (PF) of cells in the resting population that will respond to antigen stimulation by proliferation (see Fig. 3 and Note 2). This flow cytometric dye dilution method can be combined with tetramer staining and with intracellular cytokine detection in order to provide a description of T cells, on a single-cell basis, with regard to their ability to bind tetramer, synthesize cytokines, and proliferate. Results (Fig. 4) indicate that not all responding T cells do all three of these functions (5). 2. Materials 2.1. Staining of Cells With Tracking Dye for Cell Culture 1. Peripheral blood mononuclear cells (PBMCs), including lymphocytes and monocytes, prepared by Ficoll-Hypaque (Amersham Pharmacia Biotech, Piscataway, NJ) density gradient centrifugation. 2. Appropriate culture medium for the lymphocytes in question (e.g., AIM V medium [Gibco™ Invitrogen Corporation, Carlsbad, CA] with serum for human cells). 3. Protein or peptide for antigen stimulation. 4. Concanavalin A (Calbiochem brand, EMD Biosciences, San Diego, CA) or phytohemagglutinin (PHA [Sigma, St. Louis, MO]) for positive proliferation control:

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Fig. 2. A cartoon illustrating that dye intensity indicates the number of divisions that have occurred as a “specific” cell expands within a mainly resting population.

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Fig. 3. PKH 67 histograms indicating a range of PBMC responses to flu peptide after 6 d in culture. Gaussian curves modeling each generation are drawn by ModFit software. Calculated precursor frequencies (PF) for proliferation are shown. Unstimulated cells are in the histogram on the left.

5.

6. 7. 8.

Prepare a stock solution of 2 mg/mL concanavalin A (Con A) in phosphatebuffered saline (PBS) and use at 5 μg/mL final concentration; prepare a stock solution of 1 mg/mL PHA in PBS and use at 2 μg/mL final concentration. Tracking dye: PKH 26 or PKH 67 (Cell Census Plus or Cell Linker kits [Sigma]), or carboxyfluorescein diacetate succinimidyl ester (CFSE [Molecular Probes, Eugene, OR] prepared as 10 mM stock concentration in dimethyl sulfoxide [DMSO]). Fetal bovine serum (Sigma or other suppliers) or human AB serum (Nabi, Boca Raton, FL) used in stopping PKH incorporation. 12- or 24-well culture plates. 15- or 50-mL conical centrifuge tubes.

2.2. Optional Treatment on the Last Day of Culture to Retain Cytokines Intracellularly 1. Brefeldin A (Sigma): Prepare a stock solution of 1 mg/mL in ethanol and use at a final concentration of 1 μg/mL. 2. Phorbol myristic acid (PMA) and ionomycin (both from Sigma) for positive cytokine control: Prepare PMA stock solution at 1 mg/mL and use at a final concentration of 10 ng/mL; prepare ionomycin stock solution at 1 mg/mL in ethanol and use at a final concentration of 500 ng/mL.

2.3. Optional Staining After Culture Before Flow Cytometry 2.3.1. Staining for Surface Phenotype and/or Tetramer 1. Antibody against CD8 or other phenotyping marker, conjugated to fluorochrome. The fluorochromes for phenotyping and tetramer need to be spectrally compatible with the tracking dye selected.

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2. Tetramer of HLA–peptide complex conjugated to fluorochrome. 3. Washing buffer: PBS plus 1% bovine serum albumin and 0.1% sodium azide. 4. Human globulin Cohn fractions II and III (Sigma) to reduce antibody binding to Fc receptors: Prepare a stock solution of 6 mg/mL. 5. 96-Well plate.

2.3.2. Staining for Intracellular Cytokine 1. Washing buffer with 1 μg/mL of brefeldin A. 2. Washing buffer with 4% formaldehyde (Ultrapure EM Grade from Polysciences, Warrington, PA). 3. Washing buffer with 0.1% saponin (Sigma). 4. Antibody conjugated to fluorochrome for cytokine of interest and equivalent isotype control. The cytokine fluorochrome needs to be spectrally compatible with the tracking dye and with any phenotyping and tetramer-conjugated fluorochromes. 5. 96-Well plate.

2.3.3. Washing, Fixing, and Centrifugation 1. Washing buffer. 2. Washing buffer with 1% formaldehyde (Ultrapure EM Grade from Polysciences). 3. Centrifuge for washing and pelleting cells in 96-well plates.

2.4. Flow Cytometry 1. Flow cytometer capable of detecting fluorochromes in use. 2. Rainbow Beads (RCP-30-5 from Spherotech, Libertyville, IL).

2.5. Data Analysis 1. The “proliferation wizard” module in ModFit software (Verity Software House, Topsham, ME) on a PC or Mac computer is used to analyze files acquired on the flow cytometer.

3. Methods 3.1. Staining of Cells With Tracking Dye for Cell Culture Lymphocytes with monocytes (PBMCs) need to be isolated by FicollHypaque density gradient centrifugation from peripheral blood (see Notes 3 and 4). Cell preparation needs to be under sterile conditions. The final number of required PBMCs is 3 × 106 per culture well, but a recommended starting number of 5–6 × 106 is suggested anticipating a cell loss during the labeling and washing steps with either tracking dye. After isolation but before culture, the PBMCs are stained with the cell-tracking dye (PKH or CFSE). PKH 26 (551 nm abs/567 nm em) or PKH 67 (490 nm abs/504 nm em) can be chosen based on spectral compatibility with other fluorochromes used. For the choice between the PKH dyes or CFSE, see Note 5. At the end of the culture period,

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Fig. 4. Multiparameter density plots indicating PKH dye dilution and interferon-γ synthesis for tetramer-positive and tetramer-negative cells after 6 d in culture stimulated by flu peptide. On d 5, the cell suspensions were restimulated with peptide. The plots indicate that both tetramer-positive and tetramer-negative cells respond to antigen stimulation and that some cells proliferate and synthesize cytokine, some cells do neither, and some cells do one or the other.

the cells can be optionally stained for phenotype, for tetramer binding, and, internally, for cytokine. If the cells will be stained for cytokine, they need to have been restimulated with antigen for the last 16 h of culture. 3.1.1. Staining Procedure With PKH Dyes (see Notes 6 and 7) 1. Wash cells twice in serum-free medium and count with a hemocytometer. Following the second wash, aspirate the supernatant, leaving a cell pellet and 25–50 μL of serum-free medium. Resuspend the cells gently in this residual medium. 2. In a separate conical tube, dilute the PKH dye stock in “diluent C” from the Sigma Cell Census Plus kit to twice the final staining concentration (e.g., 8 μM if the final staining concentration is 4 μM). After dilution, the dye should be used immediately; any unused dye should be discarded. The concentration of dye stock should be tested in advance to maximize both the brightness and the viability of the stained cells and also to ensure that high brightness does not make spectral compensation difficult with other fluorochromes used. For human lymphocytes, the final dye concentration will be approx 4 μM. 3. Dilute the resuspended cell pellet in “diluent C” to give a final cell concentration of 2 × 107 cells/mL. A conical centrifuge tube equal in volume to more than six times the volume of the cell suspension should be used. The diluent is designed to produce even dispersal of the lipophilic dye but can be harsh on the cells. Therefore, for maximum yields, cells should not be left in this diluent any longer than necessary.

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4. Add an equal volume of the PKH dye solution to the cell suspension. Incubate the cells with the dye for 3 min at room temperature. Cell labeling is rapid, with 80% occurring within the first 15 s. For homogeneous labeling, it is important that the cells and dye be rapidly combined and gently mixed. 5. After 3 min, add an equal volume of human AB serum or fetal bovine serum (FBS) to the cell suspension to stop the integration of the dye. 6. Wash the cells three times in culture medium, count, and resuspend to 1.5 × 106 cells/mL in medium.

3.1.2. Alternate Staining Procedure With CFSE (adapted from ref. 10; see Notes 6 and 7) 1. Immediately prior to cell labeling, dilute the 10 mM stock solution of CFSE (in DMSO) to 1 mM in PBS. 2. Wash the cells twice in serum-free medium, count with a hemocytometer, and resuspend in 37°C medium at a final concentration of 5 × 107 cells/mL. Use a tube that is more than six times the volume of cells. 3. Add 2 μL of CFSE/mL of cell suspension (giving a final CFSE concentration of 2 μM ). This concentration should be tested and modified to bring about bright staining with high cell viability (if the staining is too bright, spectral compensation with other fluorochromes may be difficult). 4. Incubate the cells with the dye for 15 min at 37°C with occasional mixing. 5. After 15 min, quench the stain by the addition of five volumes of ice-cold medium with 10% FBS. 6. Let stand at room temperature for 5–10 min. 7. Wash the cells three times in medium and resuspend in medium to a concentration of 1.5 × 106 cells/mL.

3.1.3. Cell Culture (see Note 8) 1. After staining with the tracking dye, count the cells and check for viability with Trypan blue. 2. Put the cells into culture with 3 × 106 cells/well in a 24-well tissue culture plate or 5 × 106 cells per well in a 12-well tissue culture plate. The final cell concentration in either case is 1.5 × 106 cells/mL. 3. Add antigenic peptides or proteins to appropriate wells at the beginning of the culture period at a concentration known to produce proliferation. This concentration should be titered in advance with tritiated thymidine uptake or with the dye dilution assay. 4. As a positive proliferation control, add Con A at 5 μg/mL final concentration or PHA at 2 μg/mL final concentration for the last 4–5 d of the culture period to wells that have not received antigen stimulation. 5. As a negative control, use wells that contain medium without mitogen or antigen. 6. Incubate the culture plates at 37°C in 5% CO2 for 6–10 d depending on the strength of the proliferative response (see Note 9). Check cultures regularly and feed with fresh culture medium as required.

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7. If subsequent staining for intracellular cytokines, for phenotypic markers, or for tetramer binding will not be performed, centrifuge the cells down from culture, resuspend in 0.2–0.4 mL of washing buffer, and analyze directly by flow cytometry after the culture period. Alternatively, after washing the cells, resuspend them in washing buffer with 1% formaldehyde (0.2–0.4 mL). After overnight fixation at 4°C, analyze the fixed cells by flow cytometry.

3.2. Optional Treatment on the Last Day of Culture to Retain Cytokines Intracellularly If the cells are to be stained for cytokine synthesis, they need to be restimulated with antigen and treated with brefeldin A during the last day of culture so that newly synthesized cytokine will remain in the cytoplasm for detection. 1. Sixteen hours before the end of the culture period, restimulate the cells with a second addition of antigen (or nothing for the control well). 2. At the same time, add brefeldin A (1 μg/mL, final concentration) to all wells. 3. Positive control wells for cytokine synthesis receive PMA (10 ng/mL final concentration) and ionomycin (500 ng/mL final concentration).

3.3. Optional Staining After Culture Before Flow Cytometry After the culture period, the cells can be stained for tetramer binding and/or for phenotype and can then be fixed, permeabilized, and stained for cytokine synthesis, if desired (see Note 10). 3.3.1. Staining for Surface Phenotype and/or Tetramer 1. At the end of the culture period, harvest cells from the wells and pellet by centrifugation. 2. Resuspend the cells in washing buffer (or in washing buffer plus 1 μg/mL brefeldin A if the cells will be stained for cytokine). The concentration of cells after resuspension should be 3–8 × 105 cells/0.03 mL. 3. Mix the cells with an equal volume of human globulin (Cohn fractions II and III; stock solution 6 mg/mL) to block nonspecific binding to Fc receptors. 4. Add cells (3–8 × 105 cells in 0.06 mL) to individual wells of a 96-well plate and stain them at saturating concentration with tetramer (2–10 μL) for 20 min at 37°C. 5. Add phenotyping antibodies at saturating concentration (5–20 μL) for an additional 20-min incubation at 4°C (see Note 11). 6. If no cytokine staining is to follow, wash the cells three times in cold washing buffer (200 μL/well for each wash) and fix overnight at 4°C in washing buffer with 1% formaldehyde (0.2–0.4 mL). Analyze by flow cytometry the next day.

3.3.2. Staining for Intracellular Cytokine 1. If staining for intracellular cytokines is to be performed, wash the cells three times in washing buffer with brefeldin (200 μL/well for each wash) and then fix them in washing buffer with 4% formaldehyde for 20 min at room temperature.

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2. After the 20-min fixation, wash the cells three times in washing buffer containing 0.1% saponin for permeabilization. 3. Resuspend the cells in 0.1 mL of washing buffer plus 0.1% saponin; add 10 μL of Cohn globulins (6 mg/mL). 4. Add fluorochrome-conjugated anticytokine antibody or isotype-matched control antibody to the well (5–20 μL to a saturating concentration). Incubate the plate for 60 min at 4°C. 5. Wash the cells two times in washing buffer with 0.1% saponin and a final time in simple washing buffer. 6. Resuspend the cells in 0.2–0.4 mL of washing buffer with 1% formaldehyde, store overnight at 4°C, and assay on the flow cytometer the following day.

3.4. Flow Cytometry (see Note 12) 1. Laser excitation and the photomultiplier tube (PMT) bandpass filters on the flow cytometer need to be compatible with the fluorochromes selected. PKH 67 and CFSE have excitation and emission characteristics that are similar to fluorescein. PKH 26 is similar to phycoerythrin. All three dyes can be excited by a 488-nm laser. 2. Fluorescence parameters, including those for the tracking dye, are all acquired with logarithmic amplification. The PMT voltages for the tetramer, phenotyping, and cytokine parameters should be set so that the negative cells are in the bottom decade on a four-decade scale. The PMT voltage for the tracking dye parameter should be set so that the unproliferated cells are in the top decade (preferably at approx 5000 on a 1–10,000 [four-decade] relative intensity scale). 3. Forward scatter and side scatter are conventionally acquired with linear amplification. The voltage/amplification on the scatter parameters should be set so that gating can be used to exclude dead cells and debris with low forward scatter, but to include proliferating cells with high forward and side scatter (see Note 13). 4. When the assay involves multiparameter analysis, spectral compensation is important but can be difficult if the PKH or CFSE staining is very bright. Lowering the concentration of tracking dye used can make compensation easier. 5. Enough cells need to be acquired into the data file so that the least frequent cells of interest are present in high enough numbers for accurate data analysis. For example, a region could be drawn around the tetramer-positive cells or the PKH/CFSE dim cells or the cytokine-positive cells and enough cells acquired into the data file to give at least 500 cells in this gate (see Note 14). Data from all cells are stored in the list mode file. 6. Data from a mixture of Rainbow Beads of different intensities are acquired into a data file at the same voltage/amplification fluorescence settings (but with forward and side scatter settings altered so that the beads are above the forward scatter threshold).

3.5. Data Analysis Before precursor analysis, cells from the data file can be gated on phenotype and/or on cytokine and tetramer fluorescence, if appropriate. For proliferation

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and precursor frequency analysis, the “proliferation wizard” module of ModFit software is used to analyze PKH or CFSE fluorescence (see Note 15). In ModFit version 3.1 or later, the software will calculate the precursor frequencies. If earlier versions of the software are being used, then the precursor frequencies can be calculated with the following equation (see Note 16): PF =

[

k = 10

][

Σ A/2k /

k=2

k = 10

Σ A/2k

k=0

]

where PF is the precursor frequency of the gated proliferating cells, k is the number of the generation (k = 0 for the parental generation), and A is the proportion of cells in each generation. For the gated or ungated cells, the software examines the PKH or CFSE fluorescence intensity distribution, derives Gaussian curves centered on halving intensity values from the original parental intensity, and uses the above equation to calculate how many cells at the beginning of the culture period (the precursor cells) were required to account for the distribution of proliferating cells at the time of the assay (6–8). For the calculation to be accurate, the number of channels that represent a halving of fluorescence intensity needs to be known. Although, on most cytometers, the full scale of 1024 channels represents a nominal range of 4 log decades of intensity, the fluorescence scale needs to be calibrated more accurately. This can be done using beads that have been standardized according to their intensities (e.g., Rainbow Beads from Spherotech). These beads are of varying intensities and have been calibrated in terms of mean equivalents of soluble fluorochrome (MESF). After acquiring a data file for the mixture of beads with the same fluorescence settings used to acquire the cell data, use a spread sheet program to plot, on the x-axis, the channel number (on a 0–1023 scale) of the median intensity for each bead type and, on the y-axis, the log of the bead’s MESF value. The slope of this line will represent how many logs of intensity are encompassed by one fluorescence channel. Multiply the slope by 1024 to give how many logs of intensity are encompassed by the full 1024 channel scale. On standard cytometers where the full logarithmic scale represents 4 log decades, this number should be approx 4. The exact number should be entered into the “proliferation wizard” module of the ModFit software. The software can determine precursor frequencies of the proliferating and nonproliferating cells in all individually gated populations (e.g., if cytokine and tetramer staining have been used, there will be four gated populations: double negative, cytokine positive, tetramer positive, and double positive) (Fig. 5). To bring all these numbers together to describe the response potential of the resting population, further calculations are necessary. The proportion of nonprolif-

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Fig. 5. Cells can be gated on tetramer-binding and cytokine synthesis before analysis of PKH staining on the gated cells. In this example, the tetramer-positive/cytokinepositive cells are mainly proliferating and outgrowing the nonproliferating cells left behind (small peak at ~3000); the tetramer-negative/cytokine-negative cells are mainly not proliferating (large peak at ~3000).

erating cells in each of the gated populations is applied to the number of gated cells in the data file to give the number of gated cells before culture that will not proliferate. Knowing the number of gated cells that will not divide and also knowing the precursor frequency of the proliferating cells in that gate, the number of cells before culture destined to divide can be calculated. The following equations represent these calculations as performed for the results from each gated population (the example here is given for a culture that is harvested at d 6): number nonprolif cells (d 0) = [(proportion parental generation (d 6)) + (0.5 * proportion generation 2 (d 6))] * [number gated cells in data file]. number cells (d 0) destined to proliferate = [(PF cells (d 0) destined to proliferate) * (numbernonprolif cells (d 0))] / [1 – PF cells (d 0) destined to proliferate].

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Table 1 Example of Precursor Frequencies (as Percentages) of CD8+ Human T Cells, With Regard to Their Ability to Respond to Flu-Peptide Stimulation by Proliferation and/or Interferon-γ Synthesis Flu-stimulated cells Will proliferate – – + +

Control cells

Will secrete IFN-γ

TET POS

TET NEG

TET POS

TET NEG

– + – +

0.52 0.11 0.09 0.60

98.23 0.08 0.36 0.01

1.27 0.00 0.01 0.00

98.60 0.00 0.12 0.00

100%

100%

The percentages describe all the cells in the resting (d 0) population and add up to 100% for each culture condition.

This same set of calculations is applied to all the gated populations of cells individually (according to their tetramer binding and cytokine production, for example), resulting in a description of the proliferative potential of the time zero population with regard to each of the gated characteristics. The number of cells in the subpopulations are then summed so that all precursor results can be expressed as a percent of the total original, resting population (5) (see Table 1). 4. Notes 1. Tritiated thymidine uptake (either in bulk culture or in conjunction with LDA) is a common method to determine proliferative responses. The tritiated thymidine bulk method does not provide the ability to analyze precursor frequencies (a few cells dividing many times will give the same result as many cells dividing once or twice). The LDA method, although well documented (4), is cumbersome. Neither tritiated thymidine method is compatible with phenotyping of the responding cells. In addition, it has been shown, in direct comparison, that precursor frequency calculations using the LDA methodology give results that are 100-fold lower than results obtained by dye dilution methodology (6). Conventional LDA assays may underestimate precursor cells because of the possibility that the low density of factors, known and unknown, may limit proliferation of the cells of interest (9). 2. Simultaneous comparison of the dye dilution method with the ELISPOT method for cytokine synthesis and with uniparameter tetramer staining before culture indicates that all three methods give similar results for the frequency of antigenspecific cells (5) and that the dye dilution assay, therefore, reflects true antigenspecific T-cell proliferative capacity.

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3. The methods in this chapter have been developed for human lymphocytes. With minor adaptations, they should be applicable to cells from other species. 4. A purified population of CD8 or CD4 cells, combined with antigen presenting cells, can be used instead of PBMCs to increase the frequency of antigenspecific cells in wells and thus to increase the number of positive events acquired for data analysis. 5. Choice of PKH or CFSE dye: CFSE stains the proteins of cells—after penetrating into the cytoplasm of a cell it becomes conjugated to the amine-containing residues on proteins. PKH, on the other hand, is a lipophilic dye that inserts into the lipid bilayer of the outer membrane. Both dyes have the potential for killing cells or inhibiting certain cell functions. It might be argued that CFSE is potentially more toxic as it binds directly to proteins. In our hands, we have found it easier to get bright staining without loss of viability using the PKH dyes. We have also found that CFSE, even at moderate concentrations, can inhibit some cell reactions (such as the proliferative response to antigen) without losing other responses (such as response to Con A). Finally, CFSE tends to stain cells very brightly and then is lost from cells rapidly for about 24 h as unstable proteins are broken down; therefore the level of staining is not immediately stable. There are, on the other hand, two serious problems with the PKH dyes. First, they are much more expensive than CFSE. Second, they do not form separate histogram peaks defining different proliferative generations (which, under optimal conditions, are seen with CFSE staining). Therefore, with the PKH dyes, there is more dependence on using curve-fitting algorithms for data analysis (but curve-fitting is easier because the algorithm does not have to match separate peaks for each generation). 6. Concentration of the cell tracking dye for staining: The dyes need to be titrated so that cells are stained brightly but with little immediate cell death. If the cells are too bright, spectral compensation with other fluorochromes will be difficult. An ideal staining level will put the nondividing cells in the fourth decade of a fourdecade log scale, with unstained cells in the first decade. In addition, tritiated thymidine uptake should be checked with both stained and unstained cells—to confirm that staining does not inhibit proliferative capacity. 7. It is important to stain the cells with the tracking dye as uniformly as possible. Cells should be resuspended well before staining to avoid aggregates and should be mixed gently during staining. 8. By comparing the stained cells, before proliferation, with the autofluorescence level of those cells, one can determine the number of generations that can be tracked. 9. A longer culture period gives more sensitivity for detection of rare precursors as they expand during proliferation. It is necessary, however, to stop the culture before the dye on the dividing cells is diluted down to the level of autofluorescence. Therefore, longer culture periods are possible when the cells are stained brightly before culture. We have found 6–8 d to be a good culture period with antigen/peptide stimulation; however, with CFSE, where bright staining without toxicity is difficult, 8 d of culture may take the cells down to the autofluores-

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11.

12.

13.

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cence level. When using polyclonal stimulation (such as ConA), 4–6 d of culture is sufficient. With enough photodetectors on a cytometer, an unlimited number of parameters can be used for gating in this assay. For example, the method could be extended to include T-cell functional markers (e.g., multiple cytokines, chemokines, perforin/granzyme), activation markers (e.g., CD25, CD69), and markers of differentiation or migration (e.g., CD27, CD28, CD62L, CCR7). Many of these markers could be combined into a description of the complex response potential of a T-cell population. If cells are stained for tetramer without staining for internal cytokine, it is recommended that a viability stain (such as propidium iodide or ToPro3) be used to gate dead cells out of the analysis; this will increase sensitivity for detection of tetramer-positive cells by lowering the background fluorescence from dead cells. Viability staining can be done only if flow cytometry is performed on unfixed cells (it is therefore not compatible with staining for intracellular cytokines). If flow cytometry is performed on fixed cells, then dead cells can be somewhat less successfully gated out of the analysis by the use of a gate based on forward and side scatter. The sensitivity of the flow cytometric dye dilution method for proliferation precursor frequency detection is limited by three factors: the intensity of the parental generation stained with tracking dye relative to its autofluorescence, the range of intensities displayed by the logarithmic amplifier, and the ability of the flow cytometer to detect rare cells. With PKH dyes, it is usually possible to stain cells so that they are approx 1000-fold brighter than the autofluorescent level. Using a four-decade log amplifier, cells could therefore remain on scale after nine divisions (e.g., cells starting at a relative intensity of 6000 would fall to 12 after nine divisions; this would still be above the background level of 6). If we conservatively assume that a flow cytometer can detect cells that are 1% of the population, those cells that are, at the time of analysis, nine divisions away from the parental cell and are 1% of the population, were, at the time they were exposed to the stimulus, 2/105 of the original population. This method should, therefore, be able to detect precursor cells of that frequency. Less conservative opinion (11) estimates that flow cytometry can detect cells of a frequency of 1/106. For analysis, cells are gated so as to exclude dead cells with low forward scatter but to include both resting and activated lymphocytes (with high forward scatter) for further analysis. It is important to have enough cells in the data file to provide accurate precursor frequency analysis. Proliferating or cytokine-producing or tetramer-binding cells should be at least 500 in number; the data analysis will be more robust if more cells can be collected into the file. If, for example, the tetramer-binding cells are, at the end of culture, only 1% of the total number of cells, then the list mode data file needs to contain 50,000 cells to provide 500 tetramer-binding cells for analysis. Similarly, it needs to contain 200,000 cells to provide 2000 tetramerbinding cells for analysis.

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15. Data analysis: Using deconvolution algorithms is somewhat more difficult with CFSE than with PKH staining because individual histogram peaks are often visible with CFSE and the Gaussian distributions need to fit well. With PKH dyes, separate histogram peaks are usually not visible; therefore it is impossible to know whether the algorithm is exactly right (but the algorithms provide rough justice). 16. Cells having undergone two or more divisions are included in the proliferative fraction. Cell having undergone only one division are considered to be either slow growing “nonspecific” or bystander cells or, alternatively, simply a low intensity shoulder on the parental peak.

References 1. Altman, J. D., Moss, P. A., Goulder, P. J., et al. (1996) Phenotypic analysis of antigen-specific T lymphocytes. Science 274, 94–96. 2. Babcock, G. F. and Frede, S. F. (1998) Intracellular cytokines, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., et al., eds.), John Wiley & Sons, New York, pp. 9.9.1–9.9.10. 3. Herr, W., Schneider, J., Lohse, A. W., Meyer zum Buschenfelde, K. H., and Wolfel, T. (1996) Detection and quantification of blood-derived CD8+ T lymphocytes secreting tumor necrosis factor alpha in response to HLA-A2.1-binding melanoma and viral peptide antigens. J. Immunol. Methods 191, 131–142. 4. Lefkovits, I. and Waldmann, H. (1999) Limiting Dilution Analysis of Cells in the Immune System. Cambridge University Press, Cambridge. 5. Bercovici, N., Givan, A. L., Waugh, M. G., et al. (2003) Multiparameter precursor analysis of T-cell responses to antigen. J. Immunol. Methods 276, 5–17. 6. Givan, A. L., Fisher, J. L., Waugh, M., Ernstoff, M. S., and Wallace, P. K. (1999) A flow cytometric method to estimate the precursor frequencies of cells proliferating in response to specific antigens. J. Immunol. Methods 230, 99–112. 7. Song, H. K., Noorchashm, H., Lieu, Y. K., et al. (1999) Cutting edge: alloimmune responses against major and minor histocompatibility antigens: distinct division kinetics and requirement for CD28 costimulation. J. Immunol. 162, 2467–2471. 8. Wells, A. D., Gudmundsdottir, H., and Turka, L. A. (1997) Following the fate of individual T cells throughout activation and clonal expansion. Signals from T cell receptor and CD28 differentially regulate the induction and duration of a proliferative response. J. Clin. Invest. 100, 3173–3183. 9. Tough, L. C. and Sprent, J. (1998) Anti-viral immunity: spotting virus-specific T cells. Curr. Biol. 8, R498. 10. Lyons, A. B. and Doherty, K. V. (1998) Flow cytometric analysis of cell division by dye dilution, in Current Protocols in Cytometry (Robinson, J. P., Darzynkiewicz, Z., Dean, P. N., eds.), John Wiley & Sons, New York, pp. 9.11.1–9.11.9. 11. Gross, H. J., Verwer, B., Houck, D., and Recktenwald, D. (1993) Detection of rare cells at a frequency of one per million by flow cytometry. Cytometry 14, 519–526.

7 Assessment of Lymphocyte-Mediated Cytotoxicity Using Flow Cytometry Luzheng Liu, Beverly Z. Packard, Martin J. Brown, Akira Komoriya, and Mark B. Feinberg Summary Cytotoxic lymphocytes, including cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells, kill target cells by releasing granules containing perforin and granzymes, and/or via Fas–Fas ligand interactions. Both pathways lead to prompt activation within target cells of caspase cascades responsible for apoptosis induction and cell death. We have utilized cell-permeable fluorogenic caspase substrates and multiparameter flow cytometry to detect caspase activation in target cells, and applied these tools to quantify and visualize cytotoxic lymphocyte activities. This novel assay, referred to as the flow cytometric cytotoxicity (FCC) assay, is a nonradioactive single-cell-based assay that provides a more rapid, biologically informative, and sensitive approach to measure cytotoxic lymphocyte activity when compared to other assays such as the 51 chromium (51Cr) release assay. In addition, the FCC assay can be used to study CTL-mediated killing of primary target cells of different cell lineages that are frequently not amenable to study by the 51Cr release assay. Furthermore, the FCC assay enables evaluation of the phenotype and fate of both target and effector cells, and as such, provides a useful new approach to illuminate the biology of cytotoxic lymphocytes.

Key Words Apoptosis, caspase, caspase substrate, cytotoxic T lymphocyte, cytotoxicity, flow cytometry, flow cytometric cytotoxicity.

1. Introduction 1.1. Target Cell Killing Mediated by Cytotoxic Lymphocytes Cytotoxic T lymphocyte (CTL) activity is triggered by T-cell receptor recognition of an antigenic peptide/major histocompatibility complex (MHC), while natural killer (NK) cell-mediated killing is based on inhibitory or stimulatory receptor recognition of specific ligands on target cells (1,2). Although From: Methods in Molecular Biology: Flow Cytometry Protocols, 2nd ed. Edited by: T. S. Hawley and R. G. Hawley © Humana Press Inc., Totowa, NJ

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they recognize target cells through different mechanisms, both CTL and NK cells induce target cell apoptosis through either the directed exocytosis of perforin and granzymes or via ligation of “death receptors” in the Fas–Fas ligand (FasL) pathway. Both pathways of cellular cytotoxicity are mediated through the interaction of specific proteins that result in the activation of a cascade of proteases; the latter are characterized by a cysteine residue in the active site and a specificity for cleavage at an aspartic acid in the P1 position (caspases) (1). Caspases exist within nonapoptotic target cells in inactive forms. Once activated, they cleave a large variety of substrates that are responsible for the subsequent morphological (cytoskeletal, nuclear, and plasma membrane breakdown) and biochemical (DNA laddering) changes associated with apoptosis. These events ultimately lead to target cell lysis, the end point of the cytotoxic killing process. 1.2. Limitations of the Conventional CTL Assay— 51 Chromium (51Cr) Release Assay Over the past three decades, the 51Cr release assay has been widely used to quantitate cytotoxic lymphocyte activity (3). In this assay, target cells labeled with radioactive 51Cr are incubated with immune effector cells for 4–6 h. Target cell lysis is then measured by detecting radioactivity released into the culture supernatant. Although the 51Cr release assay has been widely and productively employed in numerous studies of cellular cytotoxicity, its utility is limited by a number of disadvantages (4,5). First, 51Cr release assay measures bulk CTL activity using “lytic unit” calculations that do not quantitate target cell death at the single-cell level. Within the context of bulk cell populations used in the 51Cr release assay, variations in the phenotype and function of effector and target cells cannot be assessed directly. Second, CTL killing of primary host target cells often cannot be studied directly, as only certain types of cells, mostly immortalized cell lines, can be efficiently labeled with 51Cr (6,7). Third, the sensitivity of the 51 Cr release assay is further limited by the fact that it measures only end point target cell death. Fourth, measurement of 51Cr release does not permit monitoring the physiology or fate of effector cells as they initiate and execute the killing process. Finally, radioactive materials require special licensing, handling, storage, and disposal, the combination of which substantially increases the total cost of the assay. In the hope of overcoming the limitations of available CTL assays, we sought to take advantage of the power of multiparameter flow cytometry and the advent of fluorogenic caspase substrates to develop a simple, more facile, and more informative strategy to quantify the levels and study the mechanisms of cell-mediated cytotoxicity. This chapter describes the materials and methods employed in the flow cytometric cytotoxicity (FCC) assay resulting from these efforts.

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1.3. Recent Development of Flow Cytometry-Based Assays Study Cell-Mediated Immune Response Recently developed immunologic methods including major histocompatibility complex (MHC) tetramers, intracellular cytokine detection, and enzyme-linked immunospot (ELISPOT) assays have greatly improved sensitivity to enumerate antigen-specific T cells; however, they do not assess the cytolytic function of antigen-specific CTLs (8–10). Given emerging data indicating that antigenspecific CD8+ T cells may be present in certain chronic infections (e.g., human immunodeficiency virus [HIV]) or malignancies (such as melanoma), but blocked in their ability to produce cytokines or to lyse target cells, assays that measure the complete spectrum of immune effector cell functions at the single-cell level are needed (11–14). Such assays will be essential for the development of new strategies to maximize immune responses to vaccine antigens, and to manipulate favorably host immune responses in a number of important diseases. The advantages of utilizing flow cytometric approaches to characterize and quantitate CTL killing has also been apparent to others. Toward this end, other groups have developed flow cytometry-based CTL assays wherein target cell death is assessed based on the amount of fluorochrome released from or retained in the prelabeled target cells (15), or by detection of the late stages of target cell death using intercalative DNA dyes (16). However, although these assays provide information that cannot be gleaned from standard 51Cr release assays, none of them reveals the fundamental processes responsible for the initiation and execution of target cell killing. Furthermore, none of these alternative flow cytometric CTL assays has yet been tested and compared with the 51 Cr release assay for their ability to quantitate sensitively and accurately CTL responses generated in the course of an in vivo exposure to a defined antigen. 1.4. Fluorogenic Caspase Substrates Detect Cytotoxic Lymphocyte-Induced Target Cell Apoptosis This chapter describes a flow cytometry assay that detects effector cell-induced caspase activation within individual target cells using a novel and unique class of cell-permeable fluorogenic caspase substrates (17–19). These reagents (developed by OncoImmunin, Inc., Gaithersburg, MD) are composed of two fluorophores covalently linked to 18-amino-acid peptides containing the proteolytic cleavage sites for individual caspases. In the uncleaved substrates, fluorescence is quenched owing to the formation of intramolecular excitonic dimers. On cleavage of the peptides by specific caspases, the fluorophore–fluorophore interaction is abolished, leading to an increase in fluoresence that can be detected by flow cytometry. In the FCC assay, first target cells are fluorescently labeled (to distinguish them from effector cells [see Subheading 3.1.]) and then coincubated with cyto-

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toxic effector cells. At the desired time point, medium is removed from samples and replaced with a solution containing a fluorogenic caspase substrate; the latter has spectroscopic properties complementary to those of the target cell label. Following incubation and washing, samples may be analyzed by flow cytometry or fluorescence microscopy. Cleavage of the substrate results in increased fluorescence in dying cells. This chapter uses the following model systems to illustrate the basic principles of the FCC assay: viral antigen-specific mouse CTL killing of target cells and human NK killing of both suspension and adherent human tumor cells. (Additional applications and further characterization of these probes as flow cytometry reagents can be found in Chapter 8 by Telford et al., this volume.) 1.5. Advantages of the FCC Assay Compared to the Conventional 51Cr Release Assay This assay has been shown to provide a single-cell-based, rapid, quantitative, and sensitive assay to detect lymphocyte-mediated target cell killing in various animal models (17). Unlike conventional chromium release assays, the FCC assay enables monitoring of cellular immune responses in real time and at the singlecell level using diverse fluorescence detection methods such as flow cytometry and fluorescence and confocal microscopy. Importantly, the assay can be used to study CTL-mediated killing of primary host target cells, and enables assessment of important biological details of the killing process, as well as the fate of immune effector cells during the killing process. These features should enable direct determination of whether specific subpopulations of cells can resist CTLmediated lysis (e.g., tumor cells or certain virus-infected cells) (20,21) or alternatively, induce apoptotic deletion of the CTL effectors themselves (e.g., through expression of FasL on specific tumors or immunologically privileged tissues, or as an immune evasion strategy employed by immunodeficiency viruses) (22,23). Although developed using the murine lymphocytic choriomeningitis virus (LCMV) infection model, this novel approach is readily applicable to other models such as HIV, SIV, Epstein–Barr virus (EBV) and cytomegalovirus (CMV) infections (data not shown). In all, the favorable attributes of the FCC assay may permit new insights into the pathogenesis of important infectious, malignant, and immunologic diseases that have been experimentally unapproachable previously, and provide a practical and useful method to quantitate CTL activity in basic and applied studies of cellular immune responses. 2. Materials 2.1. Preparation of Target Cells 1. Target cells: Either tumor cell lines or primary cells such as mouse splenocytes can be used to prepare a single-cell suspension. For example, EL4 cells (American Type

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Culture Collection [ATCC], Manassas, VA, cat. no. TIB-39) or A20 cells (ATCC, cat. no. TIB-208) can be used in mouse models with H-2b haplotype or H-2d haplotype, respectively. Other examples include Jurkat cells and MDA-MB-468 (ATCC, cat. no. HTB-132). Complete media (see Note 1): a. RPMI 1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum ([FBS], HyClone, Logan, VT), 100 U of penicillin G, 100 μg/mL of streptomycin sulfate, and 2 mM L-glutamine (100X stock, all from Mediatech, Herndon, VA). EL4, A20 and Jurkat cells can be maintained in this medium. b. Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% FBS. Most adherent cell lines such as MDA-MB-468 can be maintained in this medium. Trypan blue (Mediatech). Target cell labeling reagents can be used to label target cells prior to introduction of effectors (two examples are listed below): a. Celltracker™ orange CMTMR ([CTO], Molecular Probes, Eugene, OR). λex = 540 nm and λem = 566 nm. It is light sensitive. On receipt, it should be stored desiccated at –20°C until use. Avoid repeated freezing and thawing. Dissolve the lyophilized product in high-quality, anhydrous dimethyl sulfoxide ([DMSO], Sigma Chemical Co., St. Louis, MO) to a final concentration of 10 mM. Store small aliquots frozen at –20°C, desiccated, and protected from light. Avoid repeated freezing and thawing. When stored properly, both the solids and the stock solutions are stable for at least 6 mo. b. TFL2 (OncoImmunin, Inc.). On receipt, it should be stored desiccated at –20°C until use. For viral antigen-specific mouse CTL killing, synthetic peptides containing the viral CTL epitope of interest are used. An irrelevant peptide should also be employed as a negative control. High-purity peptides can be ordered from American Peptide Company, Inc. (Sunnyvale, CA). Staurosporine Streptomyces sp. (Sigma Chemical Co.). Store at 4°C. 15-mL Falcon polypropylene conical tubes with screw caps (BD Biosciences Discovery Labware, Bedford, MA).

2.2. Preparation of Effector Cells 1. Effector cells: Lymphocytes from the spleen or lymph nodes of mice acutely infected with viruses (d 5–8 postinfection) (17), the NK92 cell line (ATCC, cat. no. CRL-2407), or a CTL cell line. 2. Red blood cell (RBC) lysing buffer (Sigma Chemical Co.). 3. 50-mL Falcon polypropylene conical tubes with screw caps, 70-μm Falcon cell strainer, and 3-mL syringe (all from BD Biosciences).

2.3. Detection of Target Cell Apoptosis by Caspase Substrates 1. PhiPhiLux-G1D2 ([caspase 3-like substrate], OncoImmunin Inc.). λex = 505 nm and λem = 530 nm. It is light sensitive, but is stable in the dark at 4°C for up to 2 mo. Freeze at –20°C for longer-term storage. Keep the reagent sterile. See Note 2.

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2. Washing buffer: Dulbecco’s phosphate-buffered saline ([PBS], Invitrogen) supplemented with 2% FBS. 3. 96-well U- or V-bottom tissue culture plate with lid, and 5-mL Falcon polypropylene round-bottom tubes (fluorescence-activated cell sorter [FACS] tubes, both from BD Biosciences).

2.4. Flow Cytometry (see Note 3) 1. A flow cytometer such as the FACSCalibur (BD Biosciences Immunocytometry Systems, San Jose, CA) or Epics® XL (Beckman Coulter, Miami, FL).

2.5. Determine Cytotoxic Activity 1. FACS data analysis software such as CellQuest (BD Biosciences), FlowJo (Tree Star, San Carlos, CA), or WinMDI (Dr. Joseph Trotter, Scripps Institute, La Jolla, CA, and BD Biosciences).

3. Methods 3.1. Preparation of Target Cells (see Note 4) 1. Suspend target cells in complete RPMI 1640 medium in a 15-mL conical tube. 2. Count viable cells with the Trypan blue exclusion method. Adjust cell concentration to 2 × 106/mL. 3. Add a 0.5-mL aliquot of target cells into a FACS tube: tube A. Leave tube A on ice until sample acquisition by flow cytometer. (This will serve as the unlabeled target cell control for instrument setting of the flow cytometer.) 4. Add a 0.5-mL aliquot of target cells into a new 15-mL conical tube: tube B. Induce apoptosis by adding an apoptogen such as staurosporine at a final concentration of 1 μM. Incubate in a 37°C 5% CO2 incubator until Subheading 3.3., step 5. Conditions for apoptosis induction will vary with target cell type and apoptogen, but a good starting point is staurosporine at 1 μM for 3–5 h. (Tube B will serve as FL1 channel control for flow cytometer setting.) 5. Divide the rest of target cell suspension equally into two 15-mL conical tubes (tubes a and b). Add CTO/TFL2 into the tubes at a final concentration of 3/2 μM. Antigenic peptide is added into tube a at final concentration of 1 μM, irrelevant control peptide is added into tube b. 6. Incubate tubes a and b at 37°C 5% CO2 for 1 h with caps loosened. During this time, prepare effector cells (see Subheading 3.2.). 7. After the 1-h incubation, wash target cells at least once in at least 10-fold volume of complete RPMI 1640. 8. Resuspend cells at 2 × 106/mL in complete RPMI 1640. Leave the cells on ice until effector cells are ready. 9. Take a 0.5-mL aliquot from each of tube a and b into two FACS tubes (tubes C and D). Leave tube C on ice until sample acquisition. (This tube will serve as FL2 channel control for flow cytometer setting.) Leave tube D on ice until Subheading 3.3., step 3. (This tube will be used to measure base line target cell apoptosis.)

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3.2. Preparation of Effector Cells From Spleen or Lymph Nodes (see Notes 4 and 5) 1. Harvest spleen or/and lymph nodes on d 5–8 post-viral infection. 2. Place a 70-μm Falcon cell strainer on top of a 50-mL Falcon tube. Place freshly removed organs into the cell strainer. 3. Press the organs against bottom of the cell strainer with plunger of a 3-mL syringe until mostly fibrous tissue remains. 4. Rinse cells through the cell strainer with 20 mL of complete RPMI 1640 medium. Discard the cell strainer. 5. Centrifuge at 250g for 10 min and discard supernatant. 6. Remove RBC in spleen samples by resuspending spleen cell pellet in RBC lysing buffer (5 mL/spleen). Incubate at room temperature for 5 min. Add RPMI 1640 to fill the tube, centrifuge at 250g for 10 min. Discard the supernatant. 7. Resuspend the cell pellet in the appropriate volume of complete RPMI 1640. Count cells by trypan blue exclusion. 8. Adjust the cell concentration to 5 × 107/mL (if maximal E/T ratio is 25⬊1).

3.3. Detection of Target Cell Apoptosis by Caspase Substrates 1. Prepare serial dilutions of effector cells in 96-well U-bottomed plate for the desired E/T ratios. For example, to obtain E/T ratios as 25⬊1, 12.5⬊1, and 6.25⬊1, 100 μL/well complete RPMI 1640 is added into wells of rows B and C of the plate. Add 200 μL/well of effector cells (5 × 107/mL) into row A of the plate. Use a multichannel pipet to transfer 100 μL/well of cell suspension from row A into the corresponding wells in row B, mix by pipetting three to five times. Change tips, then transfer 100 μL/well cell suspension from row B into the corresponding wells in row C, mix well, and discard 100 μL/well cell suspension from row C. 2. Add 100 μL/well (2 × 105 cell/well) of target cell suspension into wells of the 96-well plate. Mix target cells and effector cells well by pipetting. 3. Add 200 μL of target cells in tube D (see Subheading 3.1., step 9) into one well of the 96-well plate. 4. Incubate the plate in a 37°C 5% CO2 incubator for 1–3 h (see Note 6). 5. Pellet cells by centrifuging the plate and tube B (see Subheading 3.1., step 4) at 250g. Discard the supernatant by flicking the plate and vacuum aspiration from the tube, respectively. 6. Add 75 μL/sample of caspase substrate PhiPhiLux-G1D2 and mix by gentle pipetting. From this point on, do not vortex-mix samples, as apoptotic cells can be “fragile.” 7. Incubate cells in a 37°C 5% CO2 incubator for 30 min (see Note 7). 8. Wash cells twice by adding 200 μL/sample of ice-cold washing buffer. 9. After the final wash, resuspend the cell pellets into 300 μL/sample of washing buffer.

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10. Transfer cells into FACS tubes. Label the tube containing staurosporine-treated target cells as tube B.

3.4. Flow Cytometry 1. Use tube A (unlabeled target cells) to set FL1 and FL2 channels initially, so that the fluorescence intensities of the majority of the events are between 100 and 101 on each axis. 2. Use tube B (PhiPhiLux-G1D2-labeled apoptotic target cells) to set up FL2 channel compensation. 3. Use tube C (CTO/TFL2-labeled target cells) to set up FL1 channel compensation. 4. Run the remaining samples.

3.5. Determine Cytotoxic Activity Data are analyzed by CellQuest, FlowJo, or WinMDI software to obtain quadrant statistics of distinct cell populations. The total target cell apoptosis is calculated as {(% CTO/TFL2+ caspase+ cells)/[(% CTO/TFL2+ caspase+ cells) + (% CTO/TFL2+ caspase– cells)]} × 100%. The following are a panel of representative experiments highlighting the broad applications and advantages of the FCC assay. Typical FCC data measuring antigen-specific CTL activity are shown in Fig. 1A,B (17). Spleen cells from C57BL/6 mice acutely infected with LCMV were used as effectors, and target EL4 cells were either loaded with the dominant LCMV H-2b-restricted CTL epitope NP396– 404 (Fig. 1A) or an irrelevant control peptide (Fig. 1B). Significant target cell apoptosis was detected with the FCC assay only when target EL4 cells were pulsed with the LCMV epitope NP396– 404, but not with the control epitope. The numbers at the upper right corners are the calculated percentages of target cell apoptosis. Figure 1C,D shows the direct comparison of the FCC assay with the 51Cr release assay. CTL activities against a panel of LCMV peptides were measured using the two methods in parallel. D 8 splenocytes were incubated with EL4 target cells pulsed with different peptides at various E/T ratios for 3 h (FCC assay) or 5 h (51Cr release assay). The two methods detected an identical pattern of dominance hierarchy of the CTL activities specific for different peptides. Importantly, the FCC assay was more sensitive than the 51Cr release assay in detecting the CTL response specific for the subdominant epitope NP205–212. Similarly, the FCC assay can be used to detect human CTL activity against viral antigens. In Fig. 2, a human CTL line was used as effector cells in the FCC assay. Strong killing of BLCL targets pulsed with the HIV A2-restricted epitope QR9 but not the control peptide was detected at an E/T ratio of 5⬊1. The FCC assay also provides a rapid and sensitive measurement for NK cell-mediated cytotoxicity. Jurkat cell death induced by the NK cell line NK92

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Fig. 1. Detection of LCMV antigen-specific CTL activity (17) using the FCC assay. (A,B) Spleen cells from d 8 LCMV-infected C57BL/6 were cocultured for 3 h with EL4 cells that were loaded with either the dominant LCMV CTL epitope NP396– 404 (A) or an irrelevant control peptide (B). The E/T ratio was 50⬊1. Subsequent incubation with PhiPhiLux detected strong caspase activity in target cells pulsed with the LCMV epitope NP396– 404, but not with the control peptide. The numbers at the upper right corners are the percentage of target cell apoptosis. (C,D) Comparison of CTL activities specific for a panel of LCMV epitopes measured by FCC and 51Cr release assays. CTO or 51Cr-labeled EL4 cells were pulsed with LCMV peptides NP396– 404 (䉫), GP33– 42 (䊐), GP276–286 (䉭), NP205–212 (䊊), or irrelevant peptide MT246–253 (䊉) and then cocultured with the same effectors as in (A) and (B) for 3 h (FCC assay) or 5 h (51Cr release assay). Target cell death was then assessed by either cleavage of the PhiPhiLux (C) or 51Cr release (D). Note that the curves representing CTL response specific for NP205–212 and MT246–253 overlapped in D.

was kinetically measured with a modified “rapid” protocol where the coincubation of targets and effectors was carried out in the caspase substrate solution. This modified protocol allows the detection of the onset of target cell death at considerably earlier time points. As shown in Fig. 3, significant target

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Fig. 2. Strong anti-HIV CTL activity was detected with the FCC assay. An HIVspecific T cell line was generated by stimulating PBMCs from an HLA A2+ HIV+ donor in vitro with the HIV peptide QR9. These T-cells were then coincubated with a CTO-labeled A2+ B-cell line bearing either the same peptide QR9 (A) or a control HIV peptide SL9 (B) at 5⬊1 ratios. Strong QR9-specific CTL activity was detected by the FCC assay.

cell death (50%) was detected as early as 20 min after the coincubation of effectors and targets at a 5⬊1 E/T ratio. At the end of a 2-h coincubation, 90% of the target cells were shown to be apoptotic. In addition, the FCC assay is readily convertible to a fluorescence microscopic assay to visualize the lymphocyte-mediated cytotoxic action (8). Figure 4 demonstrates the detection of NK92-mediated killing of breast carcinoma target cell line MDA-MB-468 cells using both flow cytometry (Fig. 4A,B) and confocal microscopy (Fig. 4C,D; nonapoptotic target cells are red; apoptotic target cells have both red and green fluorescence signals and therefore appear yellow). Thus, the FCC assay enables monitoring of cellular immune responses in real time and at the single-cell level using diverse fluorescence detection methods. 4. Notes 1. The character of the FBS used in cell culture can be a critical element in obtaining good results with the FCC assay protocol. It may be necessary to screen multiple lots of FBS to obtain an optimal lot that supports high effector cell activity and low target cell spontaneous apoptosis. 2. An alternative caspase substrate (for caspase 6) is used in the CyToxiLux cytotoxicity assay kit (OncoImmunin Inc.) to detect target cell apoptosis (http://www.phiphilux.com/cytotox.htm). Similar results can be obtained using the CyToxiLux kit and the protocol described in this chapter.

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Fig. 3. The FCC assay provides rapid and sensitive detection of NK cell cytotoxicity. TFL2-labeled Jurkat cells were incubated with the NK cell line NK92 at an E/T ratio of 5⬊1 for the time indicated in the presence of the caspase 6 substrate. Significant cytotoxicity (50%) was detected as early as 20 min.

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Fig. 4. The detection of NK92-mediated killing of breast carcinoma target cell line MDA-MB-468 cells using both flow cytometry (A,B) and confocal microscopy (C,D). Target cells were labeled with TFL2 and incubated without (A,C) or with (B,D) NK92 cells for 2 h in the presence of caspase 6 substrate at an E/T ratio of 5⬊1. Nonapoptotic target cells are red; apoptotic target cells have both red and green fluorescence signals and therefore appear yellow. 3. Instrument settings of flow cytometry-based assays are critical for quantitation accuracy. Because the fluorescence emissions from PhiPhiLux-G1D2 and CTO/TFL2 overlap to some extent, compensation is necessary. A significant amount of orange fluorescence is present in the PhiPhiLux-G1D2 emission, and compensation for the FL2 channel may require subtraction of 80% or more from FL1 (FL2 minus ≥80% FL1). A new version of the FCC which uses the same principles described herein but does not require compensation is now available from OncoImmunin, Inc. The only additional requirement is a flow cytometer equipped with both 488-nm and 633/635-nm laser lines.

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4. Viability of both target cells and effector cells prior to coincubation is critical for the sensitivity of the assay. Target cells should be maintained in complete medium at optimal concentration, so that baseline cell apoptosis is 675 nm (“Hoechst Red” fluorescence) following ultraviolet (UV) excitation, a rare subset of mouse bone marrow cells (30 μM (26). We have occasionally noticed this when using serum-supplemented PBS. Precipitation is not instantaneous and can be avoided by making serial dilutions quickly. If precipitation is observed, the working solution should be discarded. 2. Murine mononuclear cells, like those of most mammalian species, are denser than human mononuclear cells. While commercial density gradient media for isolation of human mononuclear cells are generally formulated at osmolarities isotonic with human plasma, Nycoprep 1.077A is specifically formulated at a lower osmolarity (265 mosm) for optimal isolation of nonhuman mammalian mononuclear cells. 3. We routinely use PBS for all cell manipulations prior to cell culture. It is possible to use bicarbonate buffered balanced salt solutions, or more complex media, but these should be buffered using N-(2-hydroxyethyl)piperazine-N-(2-ethanesulfonic acid) (HEPES). It is preferable to avoid use of buffers containing phenol red, as this dye can be excited at 488 nm and can cause cells to autofluoresce. However, these fluorescent emissions can be compensated, and we have used these buffers in the past without adversely affecting the detection of Hodull/Rhdull target cells.

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Fig. 3. Flowchart showing typical yields of nucleated cells at each step of the multiparameter cell separative strategy devised for the isolation of Hodull/Rhdull PHSC from normal murine bone marrow.

4. The weights of chemical reagents used for making up PBS are for the anhydrous form of buffer ingredients. If hydrated forms of these reagents are used the weights need to be adjusted accordingly. 5. Heat inactivation of serum for this application is adopted as a precautionary measure. Although is not strictly necessary when using highly purified antibody reagents, we do so because we have occasionally experienced significant nonspecific cell losses when using buffers supplemented with non-heat-inactivated serum especially when incubating bone marrow cells with unpurified or partially purified

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antibody supernatants. Alternately, 0.5% BSA (fraction V, tissue culture grade) can be substituted for serum as a buffer constituent. We use MACS systems as the immunomagnetic cell separation platform in our laboratory. It is equally valid to use Dynabeads for this purpose. Alternatively, cells can be labeled with a cocktail of PE-conjugated primary antibodies. In this case, hematopoietic lineage antigen positive cells can be excluded flow cytometrically in the sort gating strategy. We have often used this approach for flow cytometric analysis of Hodull/Rhdull bone marrow cells. However, because lineage positive cells constitute up to 95% of the low density cell fraction this alternative significantly extends the amount of cell sorter time required to isolate Hodull/Rhdull PHSC. We have chosen to use biotinylated antibody reagents and streptavidin beads for immunomagnetic selection based on the versatility of the primary antibody reagents in other applications in our laboratory. It is equally valid to use purified primary rat antimouse antibodies and microbead-conjugated antirat IgGs. The choice of fluorochrome conjugates will also ultimately be guided by laser configuration and fluorescence emission detection capabilities of the cell sorter. It is imperative that biotin-free buffer is used for labeling with biotinylated antibodies to prevent competition of free biotin with biotinylated antibody in the binding of the streptavidin microbeads. This buffer can be supplemented with certified biotin-free BSA, but not serum or BSA of unknown status. BSA-supplemented buffer is recommended for the immunomagnetic separation steps following antibody and immunomagnetic bead conjugation. The collection of bone marrow cells by crushing bones using a mortar and pestle rather than solely by flushing the bone shafts from both ends with cold PBS–2% HiSe using a 1-mL syringe fitted with a 23-gage needle significantly reduces the number of donor mice. Lambert et al. (49) have shown that approx 5 × 108 cells can be recovered from the entire skeleton of single adult mouse using this method. We typically harvest approx 108 cells from the pooled femurs, tibiae, and iliac crest of a single adult mouse. PHSC are intimately associated with endosteal marrow (50). Digestion of crushed bone fragments using collagenase/dispase also maximizes stem cell yield. Periodic agitation of the tube will aid dispersion of the cells if a 37°C water bath is used in place of a shaker. We routinely use 50-mL tubes for density gradient centrifugation. If preferred, gradients can be prepared in 15-mL centrifuge tubes by overlaying 6 mL of cell suspension on a 5-mL Nycoprep cushion. On average, a single 50-mL gradient tube is required for the bone marrow harvested from two mice. Although it is advisable to follow the manufacturer’s advice, a lower bead/cell ratio can be used; but the likelihood of contamination of the nonmagnetic fraction with cells expressing low levels of hematopoietic lineage antigens is increased. Typically, a CS column (capacity 2 × 108 magnetically labeled cells) is required for the bone marrow harvested from five or six mice. The manufacturer’s data sheets specify a number of flow resistors that are suitable for use with various

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MACS columns. We have found that optimal resolution of Lin– cells is achieved using a 22G flow resistor with a CS column and a 21G flow resistor if using a D column. 14. There are a number of critical variables that must be controlled to ensure an optimal enrichment of lineage-negative cells using the MACS system. The separator must be chilled, and buffers and cell suspensions kept cold. Degassing of buffers used to prime and wash MACS columns is essential to prevent the formation of air bubbles in the column or flow resistor with consequent impairment of flow rate. Likewise, it is essential that the column not be allowed to run dry during the separation procedure. 15. Temperature is an important variable that must be precisely controlled for optimal performance of efflux pumps. It is essential that buffers and media used in dye loading and efflux steps be prewarmed; and that tubes be immersed in a 37°C water bath to at least the level of the meniscus of the cell suspension during this procedure. 16. In contrast to the gating strategy used by others to isolate Hodull/Rhdull cells (11) in which this fraction is delimited by the lowest 15 percentiles of Rh123 fluorescence within the lowest 3 percentiles of Ho fluorescence, we have defined Hodull/Rhdull cells with reference to the bivariate Rh123 vs Ho fluorescence dot-plot (13). In the first strategy placement of the Rh123 sort gate is contingent on the distribution of Ho fluorescent cells. Although our approach by-and-large defines a similar population (0–14th percentile of Rh123 fluorescence within the 0–5th percentile of Ho fluorescence), we believe that definition Hodull/Rhdull cells with reference to the bivariate plot provides a more accurate and reproducible definition of the Hodull/Rhdull phenotype. However, in those instances in which the Hodull/Rhdull cell cluster is difficult to visualize in the bivariate dot-plot, we defer to the former method.

References 1. Bertoncello, I., Hodgson, G. S., and Bradley, T. R. (1985) Multiparameter analysis of transplantable hemopoietic stem cells. I. The separation and enrichment of stem cells homing to marrow and spleen on the basis of Rhodamine 123 fluorescence. Exp. Hematol. 13, 999–1006. 2. Bertoncello, I., Hodgson, G. S., and Bradley, T. R. (1988) Multiparameter analysis of transplantable hemopoietic stem cells. II. Stem cells of long-term bone marrow reconstituted recipients. Exp. Hematol. 16, 245–249. 3. Bertoncello, I., Bradley, T. R., Hodgson, G. S., and Dunlop, J. M. (1991) The resolution, enrichment, and organisation of normal bone marrow high proliferative potential colony-forming cell subsets on the basis of rhodamine 123 fluorescence. Exp. Hematol. 19, 174–178. 4. Visser, J. W., Bol, S. J., and van den Engh, G. (1981) Characterization and enrichment of murine hemopoietic stem cells by fluorescence activated cell sorting. Exp. Hematol. 9, 644–655. 5. Baines, P. and Visser, J. W. (1983) Analysis and separation of murine bone marrow stem cells by H33342 fluorescence-activated cell sorting. Exp. Hematol. 11, 701–708.

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6. Ploemacher, R. E. and Brons, N. H. (1988) Cells with marrow and spleen repopulating ability and forming spleen colonies on day 16, 12 and 8 are sequentially ordered on the basis of increasing rhodamine 123 retention. J. Cell. Physiol. 136, 531–536. 7. Pallavicini, M. G., Summers, L. J., Dean, P. N., and Gray, J. W. (1985) Enrichment of murine hemopoietic clonogenic cells by multivariate analyses and sorting. Exp. Hematol. 13, 1173–1181. 8. Neben, S., Redfearn, W. J., Parra, M., Brecher, G., and Pallavicini, M. (1991) Short- and long-term repopulation of lethally irradiated mice by bone marrow stem cells enriched on the basis of light scatter and Hoechst 33342 fluorescence. Exp. Hematol. 19, 958–967. 9. Goodell, M. A., Brose, K., Paradis, G., Conner, A. S., and Mulligan, R. C. (1996) Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo. J. Exp. Med. 183, 1797–1806. 10. Goodell, M. A., Rosenzweig, M., Kim, H., et al. (1997) Dye efflux studies suggest that hematopoietic stem cells expressing low or undetectable levels of CD34 antigen exist in multiple species. Nat. Med. 3, 1337–1345. 11. Wolf, N. S., Kone, A., Priestley, G. V., and Bartelmez, S. H. (1993) In vivo and in vitro characterization of long-term repopulating primitive hematopoietic cells isolated by sequential Hoechst 33342-rhodamine 123 FACS selection. Exp. Hematol. 21, 614–622. 12. Sitnicka, E., Ruscetti, F. W., Priestley, G. V., Wolf, N. S., and Bartelmez, S. H. (1996) Transforming growth factor beta 1 directly and reversibly inhibits the initial cell divisions of long-term repopulating hematopoietic stem cells. Blood 88, 82–88. 13. Bradford, G. B., Williams, B., Rossi, R., and Bertoncello, I. (1997) Quiescence, cycling and turnover in the primitive hematopoietic stem cell compartment. Exp. Hematol. 25, 445–453. 14. Nilsson. S., Dooner, M., Tiarks, C., Heinz-Ulrich, W., and Quesenberry, P. J. (1997) Potential and distribution of transplanted hematopoietic stem cells in a nonablated mouse model. Blood 89, 4013–4020. 15. Reddy, G. P., Tiarks, C. Y., Pang, L., Wuu, J., Hsieh, C. C., and Quesenberry, P. J. (1997) Cell cycle analysis and synchronization of pluripotent hematopoietic progenitor stem cells. Blood 90, 2293–2299. 16. Micallef, S, Ramsay, R., Williams, B., Rossi, R., Mucenski, M., and Bertoncello, I. (2000) The role of c-myb and BCL-2 in hematopoietic stem cell regulation. Exp. Hematol. 28(Suppl. 1), 68. 17. Reddy, G. P. V., McAuliffe, C. I., Pang, L., Quesenberry, P. J., and Bertoncello, I. (2002) Cytokine receptor repertoire and cytokine responsiveness of Hodull/Rhdull stem cells with differing potentials for G1/S phase progression. Exp. Hematol. 30, 792–800. 18. Spangrude, G. J. and Johnson, G. R. (1990) Resting and activated subsets of mouse multipotent hematopoietic stem cells. Proc. Natl. Acad. Sci. USA 87, 7433–7437. 19. Li, C. L. and Johnson, G. R. (1995) Murine hematopoietic stem and progenitor cells: I. Enrichment and biologic characterization. Blood 85, 1472–1479.

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20. Uchida, N., Combs, J., Chen, S., Zanjani, E., Hoffman, R., and Tsukamoto, A. (1996) Primitive human hematopoietic cells displaying differential efflux of the rhodamine 123 dye have distinct biological activities. Blood 88, 1297–1305. 21. Kim, M., Cooper, D. D., Hayes, S. F., and Spangrude, G. J. (1998) Rhodamine-123 staining in hematopoietic stem cells of young mice indicates mitochondrial activation rather than dye efflux. Blood 91, 4106–4117. 22. Kim, M., Moon, H. B., and Spangrude, G. J. (2003) Major age-related changes of mouse hematopoietic stem/progenitor cells. Ann. NY Acad. Sci. 996, 195–208. 23. Zijlmans, J. M., Visser, J. W., Kleiverda, K., Kluin, P. M., Willemze, R., and Fibbe, W. E. (1995) Modification of rhodamine staining allows identification of hematopoietic stem cells with preferential short-term or long-term bone marrowrepopulating ability. Proc. Natl. Acad. Sci. USA 92, 8901–8905. 24. Visser, J. W. and de Vries, P. (1988) Isolation of spleen-colony forming cells (CFU-s) using wheat germ agglutinin and rhodamine 123 labeling. Blood Cells 14, 369–384. 25. Huttmann, A., Liu, S. L., Boyd, A. W., and Li, C. L. (2001) Functional heterogeneity within rhodamine123(lo) Hoechst33342(lo/sp) primitive hemopoietic stem cells revealed by pyronin Y. Exp. Hematol. 29, 1109–1116. 26. Srour, E. F. and Jordan, C. T. (2002) Isolation and characterization of primitive hematopoietic cells based on their position in the cell cycle, in Hematopoietic Stem Cell Protocols (Klug, C. A. and Jordan, C. T., eds.), Humana Press, Totowa, NJ, pp. 93–111. 27. Hellman, S., Botnick, L. E., Hannon, E. C., and Vigneulle, R. M. (1978) Proliferative capacity of murine hematopoietic stem cells. Proc. Natl. Acad. Sci. USA 75, 490–494. 28. Lajtha, L. G. (1979) Stem cell concepts. Differentiation 14, 23–34. 29. Hodgson, G. S., Bradley, T. R., and Radley, J. M. (1982) The organization of hemopoietic tissue as inferred from the effects of 5-fluorouracil. Exp. Hematol. 10, 26–35. 30. Bunting, K. D. (2002) ABC transporters as phenotypic markers and functional regulators of stem cells. Stem Cells 20, 11–20. 31. Schinkel, A. H., Smit, J. J., van Tellingen, O., et al. (1994) Disruption of the mouse mdr1a P-glycoprotein gene leads to a deficiency in the blood–brain barrier and to increased sensitivity to drugs. Cell 77, 491–502. 32. Schinkel, A. H., Mayer, U., Wagenaar, E., et al. (1997) Normal viability and altered pharmacokinetics in mice lacking mdr1-type (drug-transporting) P-glycoproteins. Proc. Natl. Acad. Sci. USA 94, 4028–4033. 33. Scharenberg, C. W., Harkey, M. A., and Torok-Storb, B. (2002) The ABCG2 transporter is an efficient Hoechst 33342 efflux pump and is preferentially expressed by immature human hematopoietic progenitors. Blood 99, 507–512. 34. Zhou, S., Schuetz, J. D., Bunting, K. D., et al. (2001) The ABC transporter Bcrp1/ABCG2 is expressed in a wide variety of stem cells and is a molecular determinant of the side-population phenotype. Nat. Med. 7, 1028–1034.

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35. Zhou, S., Morris, J. J., Barnes, Y., Lan, L., Schuetz, J. D., and Sorrentino, B. P. (2002) Bcrp1 gene expression is required for normal numbers of side population stem cells in mice, and confers relative protection to mitoxantrone in hematopoietic cells in vivo. Proc. Natl. Acad. Sci. USA 99, 12,339–12,344. 36. Johnson, L. V., Walsh, M. L., and Chen, L. B. (1980) Localization of mitochondria in living cells with rhodamine 123. Proc. Natl. Acad. Sci. USA 77, 990–994. 37. Johnson, L. V., Walsh, M. L., Bockus, B. J., and Chen, L. B. (1981) Monitoring of relative mitochondrial membrane potential in living cells by fluorescence microscopy. J. Cell Biol. 88, 526–535. 38. Darzynkiewicz, Z., Staiano-Coico, L., and Melamed, M. R. (1981) Increased mitochondrial uptake of rhodamine 123 during lymphocyte stimulation. Proc. Natl. Acad. Sci. USA 78, 2383–2387. 39. Latt, S. A. and Stetten, G. (1976) Spectral studies on 33258 Hoechst and related bisbenzimidazole dyes useful for fluorescent detection of deoxyribonucleic acid synthesis. J. Histochem. Cytochem. 24, 24–33. 40. Lalande, M. E. and Miller, R. G. (1979) Fluorescence flow analysis of lymphocyte activation using Hoechst 33342 dye. J. Histochem. Cytochem. 27, 394–397. 41. Arndt-Jovin, D. J. and Jovin, T. M. (1977) Analysis and sorting of living cells according to deoxyribonucleic acid content. J. Histochem. Cytochem. 25, 585–589. 42. Watson, J. V., Nakeff, A., Chambers, S. H., and Smith, P. J. (1985) Flow cytometric fluorescence emission spectrum analysis of Hoechst-33342-stained DNA in chicken thymocytes. Cytometry 6, 310–315. 43. Smith, P. J., Nakeff, A., and Watson, J. V. (1985) Flow-cytometric detection of changes in the fluorescence emission spectrum of a vital DNA-specific dye in human tumour cells. Exp. Cell Res. 159, 37–46. 44. Smith, P. J., Morgan, S. A., and Watson, J. V. (1991) Detection of multidrug resistance and quantification of responses of human tumour cells to cytotoxic agents using flow cytometric spectral shift analysis of Hoechst 33342-DNA fluorescence. Cancer Chemother. Pharmacol. 27, 445–450. 45. Ratajczak, M. Z., Pletcher, C. H., Marlicz, W., et al. (1998) CD34+, kit+, rhodamine123(low) phenotype identifies a marrow cell population highly enriched for human hematopoietic stem cells. Leukemia 12, 942–950. 46. Leemhuis, T., Yoder, M. C., Grigsby, S., Aguero, B., Eder, P., and Srour, E. F. (1996) Isolation of primitive human bone marrow hematopoietic progenitor cells using Hoechst 33342 and Rhodamine 123. Exp. Hematol. 24, 1215–1224. 47. Szilvassy, S. J. and Cory, S. (1993) Phenotypic and functional characterization of competitive long-term repopulating hematopoietic stem cells enriched from 5-fluorouracil-treated murine marrow. Blood 81, 2310–2320. 48. Borth, N., Kral, G., and Katinger, H. (1993) Rhodamine 123 fluorescence of immortal hybridoma cell lines as a function of glucose concentration. Cytometry 14, 70–73.

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49. Lambert, J. F., Carlson, J. E., Colvin, G. A., and Quesenberry, P. J. (2000) Evaluation of mouse whole body bone marrow cellularity and distribution of hematopoietic progenitors. Exp. Hematol. 28, 1493. 50. Nilsson, S. K., Johnston, H. M., and Coverdale, J. A. (2001) Spatial localization of transplanted hemopoietic stem cells: inferences for the localization of stem cell niches. Blood 97, 2293–2299.

11 Phenotypic and Functional Analyses of CD34NEG Hematopoietic Precursors From Mobilized Peripheral Blood Douglas C. Dooley and Barbara K. Oppenlander Summary Methods are described for the characterization of CD34 antigen modulation and its relationship to cell proliferation in early human hematopoietic cells. Toward that end, quiescent primitive CD34+ and CD34NEG cells are purified from mobilized peripheral blood (MoPB). Unlike CD34NEG cells from other sources, those from MoPB grow readily in stroma-free culture, facilitating their analysis. Using a lineage-depleted, low-density mononuclear cell fraction, CD34NEGCD38NEGLINNEG and CD34+CD38NEGLINNEG cells are purified by cell sorting. Cells are cultured in serum-free medium supplemented with early acting cytokines. Up- and downmodulation of CD34 antigen can be observed within 40 h of incubation. Samples are removed for analysis of expression of CD34, CD38 and lineage-commitment antigens as well as for cell proliferation as determined by expression of Ki67 antigen and uptake of pyronin Y. This approach permits an assessment of changes in CD34 and CD38 antigen expression by primitive LINNEG cells as they are activated for growth or remain in a quiescent state.

Key Words CD34-negative, cell cycle, flow cytometry, hematopoiesis, stem cells.

1. Introduction CD34 antigen has been considered a “pan” hematopoietic cell marker, present from the earliest stages of hematopoietic differentiation. The exact function of CD34, a sialomucin, is not known, though cytoadhesion and/or differentiation have been suggested (1,2). In the laboratory, CD34 antigen has become the standard by which human hematopoietic cells have been identified, quantitated and/or purified for laboratory and clinical studies (3–5). For example, it is widely used as a surrogate marker for stem cell mobilization. Thus, it was surFrom: Methods in Molecular Biology: Flow Cytometry Protocols, 2nd ed. Edited by: T. S. Hawley and R. G. Hawley © Humana Press Inc., Totowa, NJ

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prising when Osawa et al. (6) demonstrated that murine CD34NEGLINNEG cells could reconstitute the lymphohematopoietic system. Subsequent studies identified early hematopoietic precursors in the CD34NEG fractions of human marrow, umbilical cord blood (UCB) and mobilized peripheral blood (MoPB) which possessed engrafting activity in fetal sheep and nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice (7–13). In vitro studies of human CD34NEG cells in serum-free, stroma-free culture systems has proven difficult as cells from marrow and UCB grow poorly under such conditions (10,13–16). In contrast, CD34NEG precursors from MoPB can be readily grown and offer an ideal system for studying proliferation and regulation of CD34 antigen in normal cells. Below, we describe a method for following CD34 antigen modulation and changes in proliferative status of primitive CD34NEGCD38NEGLINNEG cells and CD34+CD38NEGLINNEG cells in serum-free culture. To distinguish cycling from noncycling cells, cells are stained with pyronin y (PY) (17,18) or analyzed for expression of Ki67 antigen (19). G0 cells are both PYLOW and Ki67NEG. In contrast, proliferating cells are PYHIGH and Ki67+. The method is particularly convenient for laboratories lacking access to a UV laser-equipped flow cytometer. 2. Materials 2.1. Reagents and Media 1. Iscove’s modified Dulbecco’s medium (IMDM) (Gibco™ Invitrogen Corporation, Carlsbad, CA, cat. no. 12440-053). 2. Serum-free expansion medium (SFEM) (StemCell Technologies, Vancouver, British Columbia, Canada, cat. no. 9650). 3. Heat-inactivated fetal bovine serum (HIFBS). 4. Cytokines: rhSCF, rhFlt3 Ligand (rhFL), rhIL-3, rhIL-6, and rh-TPO. 5. Sterile 10X phosphate-buffered saline (PBS), calcium, magnesium-free (Gibco™ Invitrogen Corporation, cat. no. 14200-075), diluted to 1X with sterile distilled water. 6. DNase (deoxyribonuclease I from bovine pancreas) (Sigma-Aldrich, St. Louis, MO, cat. no. 2025). 7. Ficoll-Paque (Amersham Biosciences, Piscataway, NJ). 8. Ammonium chloride-EDTA (StemCell Technologies, cat. no. 7850). 9. Nonfluorescent antibodies from StemCell Technologies for immunomagnetic separation: The lineage-depletion reagent (Human Progenitor Enrichment Cocktail, cat. no. 14056) is used for magnetic fractionation of cells. It consists of glycophorin A (GlyA), CD2, CD3, CD14, CD16, CD19, CD24, CD56, and CD66b and includes the magnetic colloid. Also required is the CD41 tetrameric antibody complex (cat. no. 14050). 10. Fluorescent antibodies from BD Biosciences (San Jose, CA): The following fluorescein isothiocyanate (FITC)-labeled antibodies are needed: CD3, CD7, CD14,

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12. 13. 14. 15. 16. 17. 18.

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CD16, CD19, CD20, CD42a, and CD56 (all but CD7and CD42a come in their lineage cocktail, cat. no. 340546). In addition, CD38-APC, the Ki67-FITC Kit (BD Biosciences, #556026) and appropriate isotypic control antibodies are required. Fluorescent antibodies from Beckman Coulter (Miami, FL): The following are required: GlyA-FITC, CD34-PE-CY5 (clone 581, class III), and isotypic control antibodies. The following phycoerythrin (PE)-labeled antibodies are needed: GlyA, CD4, CD14, CD16, CD19, CD20, CD41, and CD56. To make a single “LIN-PE” pool, combine 100 μL of each and store in a dark bottle at 4°C. For cell analysis, use 25 μL of the pool per tube. Appropriate isotypic control antibodies are also required. Cytofix/Cytoperm Kit (BD Biosciences, cat. no. 554714). Penicillin + streptomycin liquid, 10,000 U (Sigma-Aldrich, cat. no. 15140-122). Low-density lipoproteins (LDLs) (Sigma-Aldrich, cat. no. L2139). Immuno-Brite QC beads (Beckman Coulter, cat. no. 6603473). Paraformaldehyde (PFA) (Sigma-Aldrich). Pyronin Y (PY) (Sigma-Aldrich). Hoechst 33342 (HO) (Sigma-Aldrich).

2.2. Working Solutions 1. Overnight storage medium (OSM): 10 mL of SFEM containing 100 μL of penicillin/streptomycin, 20 μL of LDL, 10 ng/mL of flt3 ligand (FL), and 10 ng/mL of stem cell factor (SCF). 2. DNase wash solution: 100 mL of sterile PBS containing 1 mg of DNase, 1% penicillin/streptomycin, and 2% HIFBS. Make fresh on the day of use. 3. Supplemented SFEM: SFEM containing 1% bovine serum albumin, 10 μg/mL of insulin, 200 μg/mL of human transferrin (iron saturated), 10– 4 M 2-mercaptoethanol, and 2 mM L-glutamine in IMDM is supplemented with 50 ng/mL of rhSCF, 50 ng/mL of rhFL, 12.5 ng/mL of rhIL-3, 10 ng/mL of rhIL-6, 100 ng/mL of rh-thrombopoietin (TPO), and 1⬊200 LDL. 4. PFA: 4% solution in PBS diluted monthly to 1%. Dilute the latter two- to fivefold into cells for fixation. 5. PBSFB: 1X PBS containing 2% HIFBS and 1% penicillin + streptomycin. 6. N-(α-hydroxyethyl)piperazine-N′-(α-ethanesulfonic acid) (HEPES) buffer: 20 mM HEPES, pH 7.2, in Hank’s balanced salt solution containing 1 g/L of glucose and 10% HIFBS. Store at 4°C. 7. HO: Stock solution is 1.6 mM. Filter-sterilize and store at 4°C, protected from light. Day of use: dilute stock solution 1⬊1000 to 1.6 μM with HEPES buffer. Keep on ice, protected from light. 8. PY: Stock solution is 100 μg/mL. Filter-sterilize and store at 4°C, protected from light. Day of use: dilute stock solution to 10 μg/mL with HEPES buffer before use. Keep on ice, protected from light.

2.3. Supplies and Equipment 1. Green Magnet (StemCell Technologies, cat. no. 11055) and green magnet stand (StemCell Technologies, cat. no. 11056).

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2. 0.5-Inch diameter column (StemCell Technologies, cat. no. 12052) or 0.6-inch diameter column (StemCell Technologies, cat. no. 12056). 3. Rainin Dynamax pump (RP-1 peristaltic pump, Rainin Instrument Co., Inc., Woburn, MA). 4. Fresh or cryopreserved MoPB cells. Sample should contain ≥4 × 108 MNC (a higher starting number facilitates later steps). 5. Flow cytometer must be equipped with two lasers capable of emitting at 488 nm (for FITC, PY, PE, and PE-CY5) and 633 nm (for allophycocyanin [APC]).

3. Methods 3.1. Overview The methods describe: (1) preparation of thawed cells, (2) isolation of a red cell-depleted mononuclear cell (MNC) fraction, (3) depletion of lineage (LIN) committed cells, (4) purification of CD34NEG and CD34+ fractions by sorting (see Note 1), (5) cell cultivation, and (6) analysis of proliferative status and phenotype. If the procedure starts with fresh MoPB cells, begin at Subheading 3.2., step 3. 3.2. Initial Preparation of Thawed Cells (see Note 2) 1. Thaw sample rapidly in a 37°C water. With continuous mixing, slowly dilute the preparation with an equal volume of cold IMDM containing 20% HIFBS. Centrifuge for 10 min at 300g at room temperature. 2. Discard supernatant and wash the cells in 30 mL of room-temperature DNase wash solution (see Note 3). Discard supernatant. Resuspend cells evenly in 10 mL of DNase wash solution. 3. Layer cells over 5 mL of Ficoll-Paque in a 15-mL tube. Centrifuge at 300g, for 25 min at room temperature (leave brake off). Collect the low density MNC band in a 50-mL tube and wash twice by centrifugation through DNase wash solution. Use 400g at room temperature for 15 min to minimize cell loss. (Use the same wash solutions for fresh and thawed cells). 4. Remove as much supernatant as possible. To hemolyze residual red cells, add 15 mL of ammonium chloride–EDTA to the pellet, mix and hold for 10 min at room temperature. Fill the tube with PBS and centrifuge for 10 min at 300g at room temperature. Wash with DNase wash solution. Before final wash, remove an aliquot for a cell count (required to determine final suspension volume). 5. Resuspend at a cell concentration of 6 × 107/mL in DNase wash solution (the permissible concentration range is 2–8 × 107 cells/mL per StemCell Technology).

3.3. Depletion of LIN+ Cells by Immunomagnetic Separation 1. First incubation: Add 100 μL of human progenitor enrichment cocktail for every 1.0 mL of cell suspension. Also add anti-CD41 at 10 μL/mL of cell suspension. Incubate for 30 min on ice. 2. Second incubation: Without washing, add 60 μL of magnetic colloid per 1.0 mL of cells. Continue incubation for an additional 30 min on ice. Do not wash the cells.

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3. The separation system, which enriches LINNEG cells by depletion of LIN+ cells, consists of a magnet, column, stand, and optional pump. The “green magnet” can be used with gravity loading or pump loading. The other magnets are designed for gravity feed of smaller quantities of cells or for single or multiple pump separations. The manufacturer recommends that for 5 × 107 to 5 × 108 cells, a 0.5-inch column should be used. For 1 × 108 to 2 × 109 cells, use a 0.6-inch column. Cell purity suffers if too small a column is used whereas yield decreases with too large a column. 4. In a laminar flow hood, lower the column into the gap of the magnet (do not insert from the front). To prime the system, slowly pump sterile PBS up through the bottom of the column until the liquid completely immerses the matrix (pump setting 1.5 for a 0.5-inch column or 3.0 for a 0.6-inch column). Remove air bubbles by sharply tapping the side of the column. Run sterile PBS (15 mL for 0.5-inch column, 25 mL with 0.6-inch column) through the column from the top and collect the waste in a discard tube. Do not allow the PBS level to fall below the level of the matrix. Replace the discard tube with a sterile collection tube (50-mL centrifuge tube). Apply the cell-colloid suspension to the top of the column, using a pump speed of 5.0 for a 0.5-inch column (10.0 for a 0.6-inch column). LINNEG cells will emerge in the column eluate. 5. To capture all LINNEG cells, run three column volumes of DNase wash solution and collect eluate. Obtain a viable count from the pooled eluates. 6. Centrifuge pooled eluates for 10 min, 300g at room temperature. Remove supernatant and resuspend cells in 10 mL of OSM. Incubate overnight in a T25 culture flask (not treated to promote adherence) at 37°C in a humidified 5% CO2 incubator. Under these conditions, cell viability can be maintained without stimulating the cells into proliferation.

3.4. Isolation of Primitive CD34NEG and CD34+ Cells 1. After overnight incubation, obtain a viable count of the cell suspension in the flask (~107 is average for an initial MoPB sample containing 4 × 108 cells). 2. Collect all but 2 × 105 cells from the T25 flask. To the flask, add 5 mL of fresh, supplemented SFEM to promote vigorous expansion of the LIN-depleted cells. These cells will be used for positive controls later in the experiment (see Subheading 3.5.1.). 3. Centrifuge the remainder of the LIN-depleted cells harvested from the T25 flask in sterile PBS in a 15-mL tube at 300g, at room temperature, 10 min. 4. Resuspend the cells in 0.5–1.0 mL of PBSFB. Aliquot the bulk of the suspension into one tube for antibody labeling. Utilize the residual cells to establish sort controls based on in-house practices. Add 2.0 mL of PBS to each tube and centrifuge them at 300g 10 min, 4°C. Discard all but 200 μL of the supernatants and resuspend the pellets in their remaining supernatants. 5. In this step, cells intended for sorting will be labeled with antibodies against CD34, CD38 and LIN antigens. LIN antigens are tagged with a commercial lineage cocktail of FITC-labeled antibodies against CD3, CD14, CD16, CD19,

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11.

Dooley and Oppenlander CD20, and CD56 supplemented with additional FITC-antibodies against CD42a, CD7, and GlyA. Thus, for every 1 × 106 cells, add 12 μL of the LIN-FITC cocktail and 15 μL each of GlyA-FITC, CD7-FITC, and CD-38-APC. Also add 10 μL of CD34-PE-CY5 and CD42a-FITC. Set up isotype controls as appropriate. Incubate for 30 min, on ice, protected from light. Wash cells twice with in PBSFB at 4°C. Resuspend the cells in PBSFB at a concentration appropriate for sorting. Keep cells cold and protected from light. After completion of in-house quality control procedures for the flow cytometer, run isotype control samples. Run a small number of the labeled cells to establish sort gates for CD34NEGCD38NEGLINNEG cells and CD34+CD38NEGLINNEG cells (Fig. 1). To optimize purification of cells lacking CD34, CD38, and LIN antigens, set gates conservatively, that is, choose regions encompassing the dimmest one-third to one-half of antigen-negative populations. Less stringent gating increases yield but may reduce purity. Sort the LIN-depleted cell suspension to obtain CD34NEGCD38NEGLINNEG and CD34+CD38NEGLINNEG fractions. Keep both the starting cell suspension and the two sorted fractions cold throughout the procedure. Obtain a viability count on sorted fractions. Set aside approx 1 × 104 cells from the CD34+ and CD34NEG fractions for step 10. Culture the remaining purified cells by transferring them to supplemented SFEM in 24-well trays in a 37°C humidified 5% CO2 incubator. Initial cell concentration should be 70%. The resulting population is uniformly small and lacking in side scatter (Fig. 1A). Thus, establishing a light scatter gate is straightforward. Cells within the light scatter gate are sent to a single-parameter histogram of LIN (Fig. 1C). LINNEG cells are assessed for expression of CD34 and CD38. In some flow cytometers (such as the Coulter EPICS Elite ESP shown in Fig. 1), cells with low fluoresence hug the axes and are not readily visible even when the bulk of the cells are brought into the middle of the histogram (Fig. 1B). Nonetheless, conservative gates can be placed such that CD34NEG cells and CD38NEG cells are defined by regions having one-half (or less) the fluoresence of isotypic controls, as shown in Fig. 1B. To observe dim cells better, the “baseline offset” feature may be used to push cells off the axes, as shown in Fig. 1D. The position of the CD34 and CD38 gates relative to isotypic controls (baseline offset feature engaged) is shown in Fig. 1F. 3.6.2. Analysis of Cell Activation and Antigen Modulation

Cells should be harvested from the cultures when both cycling and quiescent cells are present. For MoPB cells, the initial sampling time should be approx 2 d. Autofluorescence is prominent in this system and must be minimized before listmode data can be analyzed. Spurious events are readily identified by their simultaneous presence in narrow 45° diagonal regions in two-parameter plots of Ki67 (or PY) vs CD34 and CD34 vs LIN. Any event that fluoresces in both of those diagonal regions (in all three photomultiplier tubes [PMTs]) is considered to be due to autofluorescence and is eliminated by boolean gating logic. This is shown in panels B and C of Figs. 2–5, where autofluorescent events (black points) are identified and subsequently removed from all other histograms shown. Note that for a cell to be counted as an autofluorescent event, it must appear in both of the regions shown in panels B and C.

Fig. 2. Ki67 analysis of cell proliferation in a CD34+ culture. After 40 h of incubation, the CD34+CD38NEGLINNEG culture was stained for expression of Ki67 and immunophenotype. (A) Light scatter histogram. Permeabilization of cells distorts original light scatter properties of cells (compare to Fig. 4A). (B,C) Identification of autofluorescent events removed from (D–F) and (R1–R6). (D) LIN profile. (E,F) CD34 and CD38 phenotypes of LINNEG cells examined after staining with isotypic antibodies (E) or antigen-specific antibodies (F). Regions R1–R6 established to identify populations modulating expression of CD34 and CD38. (R1–R6) Ki67 expression in populations R1–R6.

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Fig. 3. Ki67 analysis of cell proliferation in the CD34NEG culture. The CD34NEGCD38NEG LINNEG sister culture was stained for expression of Ki67 and immunophenotype. See Fig. 2 legend.

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Fig. 4. PY analysis of cell proliferation in the CD34+ culture. The same CD34+CD38NEG LINNEG culture shown in Fig. 2 was stained for uptake of PY and immunophenotype. (A) Light scatter histogram. (B,C) Identification of autofluorescent events removed from (D–F) and (R1–R6). (D) LIN profile. (E,F) CD34 and CD38 phenotypes of LINNEG cells examined after staining with isotypic antibodies (E) or antigen-specific antibodies (F). Regions R1–R6 established to identify populations modulating expression of CD34 and CD38. (R1–R6) PY uptake by populations R1–R6.

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Fig. 5. PY analysis of cell proliferation in the CD34NEG culture. The CD34NEG CD38NEG LINNEG culture shown in Fig. 3 was stained for uptake of PY and immunophenotype. See Fig. 4 legend.

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Figure 2 shows the analysis of a CD34+ culture after 40 h of incubation. LINNEG cells (D) are sent to a histogram of CD38 vs CD34 (F) where events are divided into six regions (R1–R6). Most LINNEG cells expressing high levels of CD34 are CD38+ (R1). For LINNEG cells expressing CD34 at lower levels, more are CD38NEG (R4) than CD38+ (R3). Interestingly, cells that have downregulated CD34 completely are almost exclusively CD38NEG (R6). Each of the six regions was analyzed for expression of the intracellular proliferation antigen Ki67. LINNEG cells in R1 and R3 (those that retained CD34 expression and had upmodulated CD38) were actively proliferating. In contrast, LINNEG cells in R4 and R6 (CD34LO-MID to CD34NEG cells that had remained CD38NEG) were essentially quiescent. Thus, an association between CD34 and CD38 modulation and the onset of proliferation can be documented. Figure 3 shows the sister CD34NEG culture. Expression of CD34 antigen by LINNEG cells is observed (R3, R4) albeit at low levels (compare to isotypic controls in E). Almost none of the cells were proliferating, demonstrating that CD34 is upregulated quite early in activation. The use of PY to analyze the same two cultures is shown in Figs. 4 and 5. With PY, permeabilization of the cells is not required and discrete populations are resolved by lightscatter in the CD34+ culture (Fig. 4A). In the CD34NEG culture, where proliferation lagged, the cells remained small (Fig. 5A). Permeabilization did not affect CD34 versus CD38 histogram patterns (compare panel F in Figs. 2 vs 4 and in Figs. 3 vs 5). Results obtained with PY agree well with and support those obtained with Ki67. With both probes, proliferation in CD34+ cultures was maximal in cells that had upregulated CD38 and continued to express CD34 while downregulation of CD34 was associated with continued quiescence (see Note 5). Furthermore, both Ki67 and PY showed that growth lagged in the CD34NEG culture, even though CD34 antigen upregulation was beginning (see Note 6). 4. Notes 1. Cell preparation and sorting can be accomplished by one person in 2 d. However, overnight storage of the cells with low level cytokines is required. The procedure can be shortened to a single day (and overnight storage eliminated) if several people work together. 2. The methods described here should be modified for use with UCB. Slower removal of cryoprotectant is necessary with UCB. UCB contains more red blood cells (RBC) which are comparatively resistant to hemolysis. In the initial NH4Cl hemolysis step, it is important not to remove too much of the supernatant to avoid loss of leukocytes. After several washes, a distinct cell layer appears, facilitating discrimination between cells and supernatant. To achieve a RBC/WBC ratio